Starting phenix.real_space_refine on Tue Aug 26 21:54:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rdz_24428/08_2025/7rdz_24428_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rdz_24428/08_2025/7rdz_24428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rdz_24428/08_2025/7rdz_24428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rdz_24428/08_2025/7rdz_24428.map" model { file = "/net/cci-nas-00/data/ceres_data/7rdz_24428/08_2025/7rdz_24428_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rdz_24428/08_2025/7rdz_24428_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 1.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 8 6.06 5 P 73 5.49 5 Mg 1 5.21 5 S 149 5.16 5 C 13346 2.51 5 N 3637 2.21 5 O 4258 1.98 5 H 20348 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41820 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 14677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 14677 Classifications: {'peptide': 927} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Chain: "B" Number of atoms: 2813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 2813 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1150 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "D" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2846 Classifications: {'peptide': 185} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 8988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 8988 Classifications: {'peptide': 590} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 559} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 2, 'ARG:plan': 3, 'GLU:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "F" Number of atoms: 9039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 9039 Classifications: {'peptide': 590} Link IDs: {'CIS': 2, 'PTRANS': 29, 'TRANS': 558} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 2, 'ARG:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "P" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 1085 Classifications: {'RNA': 34} Modifications used: {'3*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 33} Chain: "T" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 1186 Classifications: {'RNA': 37} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna3p': 36} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4798 SG CYS A 301 62.864 45.789 121.755 1.00 96.15 S ATOM 4875 SG CYS A 306 62.319 46.731 125.414 1.00 93.70 S ATOM 4940 SG CYS A 310 63.682 43.317 124.464 1.00 90.37 S ATOM 7697 SG CYS A 487 64.702 60.717 107.944 1.00105.21 S ATOM 10214 SG CYS A 645 63.864 62.439 111.247 1.00108.56 S ATOM 10224 SG CYS A 646 62.506 58.966 110.393 1.00108.32 S ATOM 21535 SG CYS E 5 112.279 64.003 58.262 1.00167.76 S ATOM 21580 SG CYS E 8 115.479 63.775 60.042 1.00166.92 S ATOM 21855 SG CYS E 26 114.115 67.318 59.463 1.00169.68 S ATOM 21898 SG CYS E 29 115.214 65.586 56.557 1.00172.84 S ATOM 22225 SG CYS E 50 96.372 84.425 55.708 1.00176.62 S ATOM 22280 SG CYS E 55 94.916 84.881 52.233 1.00176.95 S ATOM 22534 SG CYS E 72 97.767 87.151 53.380 1.00178.82 S ATOM 21700 SG CYS E 16 104.426 67.702 51.130 1.00177.74 S ATOM 21727 SG CYS E 19 104.949 63.918 50.379 1.00176.85 S ATOM 30523 SG CYS F 5 62.163 65.025 61.033 1.00174.56 S ATOM 30568 SG CYS F 8 65.024 65.404 58.683 1.00176.01 S ATOM 30845 SG CYS F 26 64.063 68.362 60.728 1.00174.10 S ATOM 30888 SG CYS F 29 61.638 67.623 58.275 1.00176.36 S ATOM 31215 SG CYS F 50 54.166 80.340 81.512 1.00181.43 S ATOM 31270 SG CYS F 55 50.553 81.352 82.093 1.00184.98 S ATOM 31524 SG CYS F 72 52.759 83.389 79.710 1.00180.92 S ATOM 30688 SG CYS F 16 52.937 67.430 66.509 1.00177.13 S ATOM 30715 SG CYS F 19 51.352 64.361 64.869 1.00178.27 S Time building chain proxies: 6.86, per 1000 atoms: 0.16 Number of scatterers: 41820 At special positions: 0 Unit cell: (147.66, 150.87, 186.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 8 29.99 S 149 16.00 P 73 15.00 Mg 1 11.99 O 4258 8.00 N 3637 7.00 C 13346 6.00 H 20348 1.00 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: 3.56 Conformation dependent library (CDL) restraints added in 995.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 310 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 306 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 301 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 487 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 646 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 645 " pdb=" ZN E1000 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 29 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 5 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 26 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 8 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 55 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 72 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 50 " pdb=" ZN E1002 " pdb="ZN ZN E1002 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E1002 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 19 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 16 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 5 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 8 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " Number of angles added : 26 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4870 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 32 sheets defined 45.4% alpha, 12.9% beta 34 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 6.53 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 169 through 177 removed outlier: 4.301A pdb=" N ARG A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 198 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 3.922A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 5.648A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.757A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.742A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.649A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.067A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.868A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 4.036A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 687 through 710 removed outlier: 3.566A pdb=" N THR A 710 " --> pdb=" O ALA A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 753 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.508A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 804 through 808 removed outlier: 3.504A pdb=" N LYS A 807 " --> pdb=" O ASP A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.567A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 851 Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 903 removed outlier: 4.040A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 916 removed outlier: 3.837A pdb=" N TRP A 916 " --> pdb=" O SER A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 925 removed outlier: 4.217A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 28 removed outlier: 4.203A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 97 removed outlier: 3.852A pdb=" N MET B 55 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 removed outlier: 3.533A pdb=" N ALA B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 143 removed outlier: 3.848A pdb=" N ASP B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 2 through 20 Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.605A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 32 through 82 removed outlier: 3.605A pdb=" N MET D 55 " --> pdb=" O ARG D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 99 removed outlier: 3.607A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 141 Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'E' and resid 26 through 37 removed outlier: 3.542A pdb=" N SER E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 63 Processing helix chain 'E' and resid 93 through 97 removed outlier: 3.954A pdb=" N CYS E 97 " --> pdb=" O LYS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 112 removed outlier: 3.537A pdb=" N PHE E 106 " --> pdb=" O ASN E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 124 removed outlier: 4.262A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 121 " --> pdb=" O ALA E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 146 removed outlier: 3.638A pdb=" N LYS E 146 " --> pdb=" O GLU E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'E' and resid 262 through 264 No H-bonds generated for 'chain 'E' and resid 262 through 264' Processing helix chain 'E' and resid 265 through 275 Processing helix chain 'E' and resid 287 through 299 removed outlier: 3.911A pdb=" N ILE E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 325 Processing helix chain 'E' and resid 376 through 379 Processing helix chain 'E' and resid 380 through 390 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 432 Processing helix chain 'E' and resid 445 through 456 removed outlier: 3.505A pdb=" N VAL E 449 " --> pdb=" O PRO E 445 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL E 456 " --> pdb=" O VAL E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 499 Processing helix chain 'E' and resid 503 through 507 removed outlier: 3.812A pdb=" N ARG E 507 " --> pdb=" O PRO E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 522 Processing helix chain 'E' and resid 522 through 527 Processing helix chain 'E' and resid 532 through 537 removed outlier: 3.552A pdb=" N GLN E 537 " --> pdb=" O VAL E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 566 Processing helix chain 'E' and resid 578 through 585 removed outlier: 3.535A pdb=" N LEU E 585 " --> pdb=" O LEU E 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 37 Processing helix chain 'F' and resid 72 through 76 removed outlier: 3.947A pdb=" N LYS F 76 " --> pdb=" O LYS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.838A pdb=" N ALA F 108 " --> pdb=" O THR F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 125 removed outlier: 4.417A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 148 removed outlier: 3.828A pdb=" N SER F 148 " --> pdb=" O THR F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 264 No H-bonds generated for 'chain 'F' and resid 262 through 264' Processing helix chain 'F' and resid 265 through 273 Processing helix chain 'F' and resid 287 through 299 Processing helix chain 'F' and resid 310 through 325 removed outlier: 3.544A pdb=" N VAL F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 423 through 433 Processing helix chain 'F' and resid 445 through 456 removed outlier: 3.938A pdb=" N VAL F 456 " --> pdb=" O VAL F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 499 removed outlier: 3.693A pdb=" N ILE F 493 " --> pdb=" O ASN F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 526 removed outlier: 3.894A pdb=" N SER F 523 " --> pdb=" O ASN F 519 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS F 524 " --> pdb=" O ALA F 520 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE F 525 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU F 526 " --> pdb=" O ALA F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 566 Processing helix chain 'F' and resid 578 through 583 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.287A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASP A 60 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ILE A 66 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 removed outlier: 7.318A pdb=" N ASP A 29 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ASN A 52 " --> pdb=" O ASP A 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.571A pdb=" N GLY A 203 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.779A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.844A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.779A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 560 removed outlier: 6.506A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 755 through 758 Processing sheet with id=AB1, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB2, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.617A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB4, first strand: chain 'E' and resid 24 through 25 removed outlier: 3.594A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AB6, first strand: chain 'E' and resid 84 through 85 Processing sheet with id=AB7, first strand: chain 'E' and resid 152 through 154 Processing sheet with id=AB8, first strand: chain 'E' and resid 162 through 163 Processing sheet with id=AB9, first strand: chain 'E' and resid 212 through 213 Processing sheet with id=AC1, first strand: chain 'E' and resid 347 through 348 removed outlier: 4.013A pdb=" N ARG E 332 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER E 331 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N THR E 359 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE E 304 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N CYS E 358 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR E 306 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR E 367 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA E 393 " --> pdb=" O THR E 367 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP E 369 " --> pdb=" O ALA E 393 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 471 through 475 removed outlier: 3.939A pdb=" N VAL E 544 " --> pdb=" O GLY E 571 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 481 through 482 Processing sheet with id=AC4, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AC5, first strand: chain 'F' and resid 14 through 15 removed outlier: 3.868A pdb=" N LEU F 14 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AC7, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AC8, first strand: chain 'F' and resid 152 through 154 Processing sheet with id=AC9, first strand: chain 'F' and resid 162 through 163 Processing sheet with id=AD1, first strand: chain 'F' and resid 197 through 198 Processing sheet with id=AD2, first strand: chain 'F' and resid 330 through 332 removed outlier: 6.423A pdb=" N SER F 331 " --> pdb=" O PHE F 357 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N THR F 359 " --> pdb=" O SER F 331 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE F 304 " --> pdb=" O VAL F 356 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N CYS F 358 " --> pdb=" O ILE F 304 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N TYR F 306 " --> pdb=" O CYS F 358 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL F 371 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE F 399 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE F 373 " --> pdb=" O ILE F 399 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N SER F 278 " --> pdb=" O TYR F 398 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 366 through 367 removed outlier: 7.139A pdb=" N THR F 366 " --> pdb=" O ARG F 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 470 through 471 removed outlier: 7.046A pdb=" N GLN F 470 " --> pdb=" O ILE F 572 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N CYS F 574 " --> pdb=" O GLN F 470 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET F 474 " --> pdb=" O CYS F 574 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 470 through 471 removed outlier: 7.046A pdb=" N GLN F 470 " --> pdb=" O ILE F 572 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N CYS F 574 " --> pdb=" O GLN F 470 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU F 573 " --> pdb=" O VAL F 544 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL F 510 " --> pdb=" O ILE F 545 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N THR F 547 " --> pdb=" O VAL F 510 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE F 512 " --> pdb=" O THR F 547 " (cutoff:3.500A) 908 hydrogen bonds defined for protein. 2481 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 9.57 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20285 1.03 - 1.23: 316 1.23 - 1.43: 9302 1.43 - 1.62: 12307 1.62 - 1.82: 210 Bond restraints: 42420 Sorted by residual: bond pdb=" N ALA E 1 " pdb=" CA ALA E 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" N ASN F 190 " pdb=" CA ASN F 190 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N ALA F 1 " pdb=" CA ALA F 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" N SER C 1 " pdb=" CA SER C 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+00 bond pdb=" C LYS F 189 " pdb=" N ASN F 190 " ideal model delta sigma weight residual 1.329 1.350 -0.021 1.40e-02 5.10e+03 2.26e+00 ... (remaining 42415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 76027 2.65 - 5.30: 380 5.30 - 7.95: 19 7.95 - 10.60: 0 10.60 - 13.25: 2 Bond angle restraints: 76428 Sorted by residual: angle pdb=" C LYS F 189 " pdb=" N ASN F 190 " pdb=" CA ASN F 190 " ideal model delta sigma weight residual 121.70 134.95 -13.25 1.80e+00 3.09e-01 5.42e+01 angle pdb=" C LYS E 189 " pdb=" N ASN E 190 " pdb=" CA ASN E 190 " ideal model delta sigma weight residual 121.70 132.89 -11.19 1.80e+00 3.09e-01 3.87e+01 angle pdb=" N LYS E 189 " pdb=" CA LYS E 189 " pdb=" C LYS E 189 " ideal model delta sigma weight residual 110.80 118.48 -7.68 2.13e+00 2.20e-01 1.30e+01 angle pdb=" N VAL E 570 " pdb=" CA VAL E 570 " pdb=" C VAL E 570 " ideal model delta sigma weight residual 113.53 110.11 3.42 9.80e-01 1.04e+00 1.22e+01 angle pdb=" CA LYS F 189 " pdb=" C LYS F 189 " pdb=" N ASN F 190 " ideal model delta sigma weight residual 116.84 122.65 -5.81 1.71e+00 3.42e-01 1.15e+01 ... (remaining 76423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.50: 19672 32.50 - 65.00: 563 65.00 - 97.51: 32 97.51 - 130.01: 1 130.01 - 162.51: 2 Dihedral angle restraints: 20270 sinusoidal: 11351 harmonic: 8919 Sorted by residual: dihedral pdb=" CA ASN F 190 " pdb=" C ASN F 190 " pdb=" N SER F 191 " pdb=" CA SER F 191 " ideal model delta harmonic sigma weight residual 180.00 138.69 41.31 0 5.00e+00 4.00e-02 6.83e+01 dihedral pdb=" CA LYS F 189 " pdb=" C LYS F 189 " pdb=" N ASN F 190 " pdb=" CA ASN F 190 " ideal model delta harmonic sigma weight residual 0.00 38.45 -38.45 0 5.00e+00 4.00e-02 5.91e+01 dihedral pdb=" CA LYS E 189 " pdb=" C LYS E 189 " pdb=" N ASN E 190 " pdb=" CA ASN E 190 " ideal model delta harmonic sigma weight residual 0.00 36.39 -36.39 0 5.00e+00 4.00e-02 5.30e+01 ... (remaining 20267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2727 0.040 - 0.079: 597 0.079 - 0.119: 172 0.119 - 0.158: 25 0.158 - 0.198: 4 Chirality restraints: 3525 Sorted by residual: chirality pdb=" CA LYS E 189 " pdb=" N LYS E 189 " pdb=" C LYS E 189 " pdb=" CB LYS E 189 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" CA ASN F 190 " pdb=" N ASN F 190 " pdb=" C ASN F 190 " pdb=" CB ASN F 190 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CA ASN E 190 " pdb=" N ASN E 190 " pdb=" C ASN E 190 " pdb=" CB ASN E 190 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 3522 not shown) Planarity restraints: 6105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS F 444 " -0.035 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO F 445 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO F 445 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 445 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 758 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C LEU A 758 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU A 758 " 0.011 2.00e-02 2.50e+03 pdb=" N SER A 759 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 76 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO E 77 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO E 77 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 77 " -0.023 5.00e-02 4.00e+02 ... (remaining 6102 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1778 2.17 - 2.78: 81403 2.78 - 3.39: 116482 3.39 - 3.99: 150010 3.99 - 4.60: 231341 Nonbonded interactions: 581014 Sorted by model distance: nonbonded pdb=" H LYS E 218 " pdb=" O HIS F 245 " model vdw 1.566 2.450 nonbonded pdb=" O ALA F 152 " pdb=" H PHE F 225 " model vdw 1.573 2.450 nonbonded pdb=" O SER D 173 " pdb=" HG SER D 177 " model vdw 1.592 2.450 nonbonded pdb=" OD1 ASP E 534 " pdb="HH12 ARG E 560 " model vdw 1.620 2.450 nonbonded pdb=" H ASN F 51 " pdb=" O TYR F 70 " model vdw 1.637 2.450 ... (remaining 581009 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 'B' and ((resid 7 and (name N or name CA or name C or name O or name CB o \ r name OG or name HA or name HB2 or name HB3 or name HG )) or resid 8 through 22 \ or (resid 23 through 24 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 25 through 191)) selection = (chain 'D' and (resid 7 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 33 through 35 or (resid 3 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 37 through 38 or (resid 39 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 40 through 47 or (resid 48 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 49 \ through 72 or (resid 73 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name OE1 or name NE2 or name H or name HA or name HB2 or \ name HB3 or name HG2 or name HG3)) or resid 74 through 191)) } ncs_group { reference = (chain 'E' and (resid 1 through 440 or (resid 441 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 442 through 1002)) selection = (chain 'F' and (resid 1 through 20 or (resid 21 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 o \ r name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 22 throug \ h 101 or (resid 102 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 103 through 182 or (resid 183 and (name N or name CA \ or name C or name O or name CB or name OG1 or name CG2 or name H or name HA or n \ ame HB or name HG21 or name HG22 or name HG23)) or resid 184 through 216 or (res \ id 217 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH or name H or name \ HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2)) or \ resid 218 through 229 or (resid 230 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 231 through 232 or (resid 233 and (na \ me N or name CA or name C or name O or name CB or name H or name HA or name HB2 \ or name HB3)) or resid 234 or (resid 235 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA or name HB2 or name HB3)) or resid 236 throu \ gh 523 or (resid 524 and (name N or name CA or name C or name O or name CB or na \ me H or name HA or name HB2 or name HB3)) or resid 525 through 1002)) } 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 group one per residue 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.260 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 47.390 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 : 0.004 0.047 22104 Z= 0.178 Angle : 0.632 13.252 30355 Z= 0.357 Chirality : 0.038 0.198 3525 Planarity : 0.003 0.054 3608 Dihedral : 13.795 162.511 8445 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.55 (0.17), residues: 2539 helix: 0.83 (0.17), residues: 1005 sheet: -0.77 (0.30), residues: 291 loop : -1.27 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 80 TYR 0.016 0.001 TYR A 903 PHE 0.015 0.001 PHE A 881 TRP 0.017 0.001 TRP A 916 HIS 0.006 0.001 HIS E 290 Details of bonding type rmsd covalent geometry : bond 0.00357 (22072) covalent geometry : angle 0.61688 (30329) hydrogen bonds : bond 0.16213 ( 980) hydrogen bonds : angle 6.15993 ( 2643) metal coordination : bond 0.01178 ( 32) metal coordination : angle 4.72901 ( 26) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue MET 233 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue LYS 524 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.776 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8171 (tm-30) REVERT: E 81 PHE cc_start: 0.6960 (m-80) cc_final: 0.6670 (m-80) REVERT: E 105 ASP cc_start: 0.8691 (t70) cc_final: 0.8329 (t0) REVERT: E 106 PHE cc_start: 0.9217 (t80) cc_final: 0.8892 (t80) REVERT: E 182 PHE cc_start: 0.8780 (m-80) cc_final: 0.8383 (m-80) REVERT: E 545 ILE cc_start: 0.8458 (mm) cc_final: 0.8241 (mm) REVERT: E 574 CYS cc_start: 0.8580 (m) cc_final: 0.6776 (p) REVERT: F 89 VAL cc_start: 0.9128 (t) cc_final: 0.8850 (t) REVERT: F 363 LEU cc_start: 0.9472 (mt) cc_final: 0.9211 (mt) REVERT: F 426 CYS cc_start: 0.8795 (m) cc_final: 0.8579 (m) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.3232 time to fit residues: 114.2682 Evaluate side-chains 173 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 258 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 822 GLN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 559 ASN ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.081101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.055219 restraints weight = 291987.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.057708 restraints weight = 104809.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.059231 restraints weight = 55538.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.060116 restraints weight = 37229.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.060629 restraints weight = 29178.213| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22104 Z= 0.256 Angle : 0.619 12.518 30355 Z= 0.329 Chirality : 0.039 0.187 3525 Planarity : 0.004 0.066 3608 Dihedral : 12.522 140.587 3880 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.55 % Allowed : 4.57 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.70 (0.17), residues: 2539 helix: 0.76 (0.16), residues: 1014 sheet: -0.81 (0.30), residues: 292 loop : -1.42 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 567 TYR 0.019 0.001 TYR D 135 PHE 0.014 0.001 PHE F 90 TRP 0.012 0.001 TRP E 114 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00529 (22072) covalent geometry : angle 0.59802 (30329) hydrogen bonds : bond 0.05342 ( 980) hydrogen bonds : angle 5.22867 ( 2643) metal coordination : bond 0.01557 ( 32) metal coordination : angle 5.52484 ( 26) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue MET 233 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue LYS 524 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 1.165 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 899 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7143 (mpt) REVERT: B 67 MET cc_start: 0.9134 (mmp) cc_final: 0.8387 (mmp) REVERT: B 70 MET cc_start: 0.9240 (ttp) cc_final: 0.9009 (ptt) REVERT: D 48 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8167 (tm-30) REVERT: E 68 MET cc_start: 0.8753 (tmm) cc_final: 0.8489 (tmm) REVERT: E 106 PHE cc_start: 0.9286 (t80) cc_final: 0.8994 (t80) REVERT: E 182 PHE cc_start: 0.8966 (m-80) cc_final: 0.8764 (m-80) REVERT: E 574 CYS cc_start: 0.8529 (m) cc_final: 0.6820 (p) outliers start: 12 outliers final: 9 residues processed: 177 average time/residue: 0.3347 time to fit residues: 91.2051 Evaluate side-chains 164 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 559 ASN Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 561 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 104 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 256 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 189 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN A 822 GLN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 GLN F 404 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.081182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.055385 restraints weight = 291028.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.057943 restraints weight = 104279.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.059471 restraints weight = 55041.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.060352 restraints weight = 36768.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.060852 restraints weight = 28851.584| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22104 Z= 0.176 Angle : 0.560 12.470 30355 Z= 0.291 Chirality : 0.038 0.196 3525 Planarity : 0.003 0.044 3608 Dihedral : 12.376 112.521 3880 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.64 % Allowed : 5.72 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.17), residues: 2539 helix: 0.92 (0.16), residues: 1019 sheet: -0.87 (0.30), residues: 283 loop : -1.44 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 129 TYR 0.019 0.001 TYR E 269 PHE 0.014 0.001 PHE E 81 TRP 0.010 0.001 TRP A 916 HIS 0.004 0.001 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00365 (22072) covalent geometry : angle 0.53730 (30329) hydrogen bonds : bond 0.04791 ( 980) hydrogen bonds : angle 4.89268 ( 2643) metal coordination : bond 0.00909 ( 32) metal coordination : angle 5.38377 ( 26) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue MET 233 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue LYS 524 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.769 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 899 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7149 (mpt) REVERT: B 67 MET cc_start: 0.9138 (mmp) cc_final: 0.8283 (mmp) REVERT: D 48 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8107 (tm-30) REVERT: E 68 MET cc_start: 0.8738 (tmm) cc_final: 0.8446 (tmm) REVERT: E 106 PHE cc_start: 0.9166 (t80) cc_final: 0.8933 (t80) REVERT: E 182 PHE cc_start: 0.9002 (m-80) cc_final: 0.8594 (m-80) REVERT: E 200 PHE cc_start: 0.8021 (m-80) cc_final: 0.7771 (m-80) REVERT: E 574 CYS cc_start: 0.8524 (m) cc_final: 0.6794 (p) outliers start: 14 outliers final: 12 residues processed: 167 average time/residue: 0.2976 time to fit residues: 78.4974 Evaluate side-chains 169 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 561 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 245 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 234 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 822 GLN ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 GLN F 559 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.079430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.053687 restraints weight = 284609.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.056164 restraints weight = 105018.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.057620 restraints weight = 56221.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.058482 restraints weight = 37877.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.058998 restraints weight = 29783.661| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22104 Z= 0.178 Angle : 0.553 13.247 30355 Z= 0.286 Chirality : 0.038 0.206 3525 Planarity : 0.003 0.043 3608 Dihedral : 12.254 111.922 3880 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.59 % Allowed : 6.86 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.53 (0.17), residues: 2539 helix: 1.06 (0.16), residues: 1019 sheet: -0.85 (0.30), residues: 285 loop : -1.45 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 567 TYR 0.016 0.001 TYR D 135 PHE 0.016 0.001 PHE E 81 TRP 0.010 0.001 TRP A 916 HIS 0.004 0.001 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00372 (22072) covalent geometry : angle 0.52784 (30329) hydrogen bonds : bond 0.04367 ( 980) hydrogen bonds : angle 4.73882 ( 2643) metal coordination : bond 0.00890 ( 32) metal coordination : angle 5.62178 ( 26) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue MET 233 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue LYS 524 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Evaluate side-chains 168 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 1.105 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: 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: symmetry clash REVERT: A 899 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7201 (mpt) REVERT: B 67 MET cc_start: 0.9176 (mmp) cc_final: 0.8849 (mmp) REVERT: D 48 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8133 (tm-30) REVERT: E 30 CYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8308 (p) REVERT: E 106 PHE cc_start: 0.9181 (t80) cc_final: 0.8946 (t80) REVERT: E 182 PHE cc_start: 0.9071 (m-80) cc_final: 0.8652 (m-80) REVERT: E 200 PHE cc_start: 0.8096 (m-80) cc_final: 0.7815 (m-80) REVERT: E 398 TYR cc_start: 0.8765 (m-80) cc_final: 0.8419 (m-80) REVERT: E 574 CYS cc_start: 0.8519 (m) cc_final: 0.6734 (p) REVERT: F 422 PHE cc_start: 0.7974 (m-10) cc_final: 0.7712 (m-10) outliers start: 13 outliers final: 10 residues processed: 161 average time/residue: 0.3164 time to fit residues: 79.7749 Evaluate side-chains 162 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 561 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 114 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 245 optimal weight: 5.9990 chunk 234 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 GLN A 650 HIS A 822 GLN E 265 ASN E 559 ASN ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.079199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.053350 restraints weight = 287393.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.055747 restraints weight = 105414.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.057204 restraints weight = 56641.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.058075 restraints weight = 38366.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.058572 restraints weight = 30241.617| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22104 Z= 0.184 Angle : 0.554 13.401 30355 Z= 0.286 Chirality : 0.038 0.213 3525 Planarity : 0.003 0.045 3608 Dihedral : 12.239 111.619 3880 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.82 % Allowed : 7.32 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.50 (0.17), residues: 2539 helix: 1.14 (0.16), residues: 1019 sheet: -0.84 (0.30), residues: 280 loop : -1.50 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 129 TYR 0.017 0.001 TYR D 135 PHE 0.029 0.001 PHE E 291 TRP 0.009 0.001 TRP A 916 HIS 0.004 0.001 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00384 (22072) covalent geometry : angle 0.52874 (30329) hydrogen bonds : bond 0.04295 ( 980) hydrogen bonds : angle 4.69631 ( 2643) metal coordination : bond 0.00859 ( 32) metal coordination : angle 5.68477 ( 26) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue MET 233 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue LYS 524 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.799 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: 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: symmetry clash REVERT: A 899 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7272 (mpt) REVERT: D 48 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8186 (tm-30) REVERT: E 30 CYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8348 (p) REVERT: E 68 MET cc_start: 0.8665 (tmm) cc_final: 0.8461 (tmm) REVERT: E 106 PHE cc_start: 0.9170 (t80) cc_final: 0.8936 (t80) REVERT: E 182 PHE cc_start: 0.9065 (m-80) cc_final: 0.8662 (m-80) REVERT: E 200 PHE cc_start: 0.8245 (m-10) cc_final: 0.7948 (m-80) REVERT: E 398 TYR cc_start: 0.8781 (m-80) cc_final: 0.8447 (m-80) REVERT: E 574 CYS cc_start: 0.8565 (m) cc_final: 0.6811 (p) outliers start: 18 outliers final: 14 residues processed: 161 average time/residue: 0.3252 time to fit residues: 81.5054 Evaluate side-chains 168 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 559 ASN Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 561 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 4 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 242 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 195 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 265 ASN ** E 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 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 = 0.4011 r_free = 0.4011 target = 0.079548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.053833 restraints weight = 284248.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.056256 restraints weight = 104348.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.057735 restraints weight = 55767.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.058615 restraints weight = 37664.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.059122 restraints weight = 29504.989| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22104 Z= 0.140 Angle : 0.530 12.876 30355 Z= 0.272 Chirality : 0.037 0.215 3525 Planarity : 0.003 0.045 3608 Dihedral : 12.208 110.946 3880 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.91 % Allowed : 7.73 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.35 (0.17), residues: 2539 helix: 1.29 (0.17), residues: 1021 sheet: -0.82 (0.30), residues: 275 loop : -1.44 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 560 TYR 0.015 0.001 TYR D 135 PHE 0.014 0.001 PHE E 291 TRP 0.010 0.001 TRP A 916 HIS 0.003 0.001 HIS E 33 Details of bonding type rmsd covalent geometry : bond 0.00294 (22072) covalent geometry : angle 0.50529 (30329) hydrogen bonds : bond 0.04121 ( 980) hydrogen bonds : angle 4.52885 ( 2643) metal coordination : bond 0.00654 ( 32) metal coordination : angle 5.47492 ( 26) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue MET 233 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue LYS 524 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 1.066 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: 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 899 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7246 (mpt) REVERT: D 48 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8196 (tm-30) REVERT: E 30 CYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8310 (p) REVERT: E 68 MET cc_start: 0.8648 (tmm) cc_final: 0.8422 (tmm) REVERT: E 106 PHE cc_start: 0.9153 (t80) cc_final: 0.8915 (t80) REVERT: E 182 PHE cc_start: 0.9041 (m-80) cc_final: 0.8636 (m-80) REVERT: E 200 PHE cc_start: 0.8254 (m-10) cc_final: 0.7939 (m-80) REVERT: E 398 TYR cc_start: 0.8770 (m-80) cc_final: 0.8437 (m-80) REVERT: E 574 CYS cc_start: 0.8529 (m) cc_final: 0.6758 (p) outliers start: 20 outliers final: 15 residues processed: 167 average time/residue: 0.2854 time to fit residues: 74.7299 Evaluate side-chains 168 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 559 ASN Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 561 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 28 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 203 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 557 ASN ** F 257 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 = 0.4010 r_free = 0.4010 target = 0.079365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.053578 restraints weight = 284620.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.056015 restraints weight = 105390.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.057453 restraints weight = 56490.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.058327 restraints weight = 38225.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.058841 restraints weight = 30061.782| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22104 Z= 0.149 Angle : 0.533 12.925 30355 Z= 0.273 Chirality : 0.037 0.216 3525 Planarity : 0.003 0.046 3608 Dihedral : 12.172 110.796 3880 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.96 % Allowed : 8.37 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.36 (0.17), residues: 2539 helix: 1.31 (0.17), residues: 1022 sheet: -0.86 (0.29), residues: 287 loop : -1.46 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 129 TYR 0.015 0.001 TYR D 135 PHE 0.029 0.001 PHE E 291 TRP 0.010 0.001 TRP A 916 HIS 0.003 0.001 HIS E 33 Details of bonding type rmsd covalent geometry : bond 0.00312 (22072) covalent geometry : angle 0.50859 (30329) hydrogen bonds : bond 0.04094 ( 980) hydrogen bonds : angle 4.49862 ( 2643) metal coordination : bond 0.00686 ( 32) metal coordination : angle 5.45586 ( 26) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue MET 233 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue LYS 524 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.662 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: 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 899 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7257 (mpt) REVERT: D 48 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8177 (tm-30) REVERT: E 30 CYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8316 (p) REVERT: E 68 MET cc_start: 0.8639 (tmm) cc_final: 0.8412 (tmm) REVERT: E 106 PHE cc_start: 0.9150 (t80) cc_final: 0.8919 (t80) REVERT: E 182 PHE cc_start: 0.9052 (m-80) cc_final: 0.8657 (m-80) REVERT: E 200 PHE cc_start: 0.8267 (m-10) cc_final: 0.7939 (m-80) REVERT: E 398 TYR cc_start: 0.8771 (m-80) cc_final: 0.8449 (m-80) REVERT: E 574 CYS cc_start: 0.8517 (m) cc_final: 0.6748 (p) outliers start: 21 outliers final: 17 residues processed: 162 average time/residue: 0.3317 time to fit residues: 84.5045 Evaluate side-chains 168 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 559 ASN Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 561 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 229 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 231 optimal weight: 5.9990 chunk 91 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 214 optimal weight: 8.9990 chunk 227 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 822 GLN E 557 ASN F 257 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.079793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.054009 restraints weight = 284425.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.056436 restraints weight = 104498.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.057942 restraints weight = 56156.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.058809 restraints weight = 37805.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.059317 restraints weight = 29745.958| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22104 Z= 0.112 Angle : 0.519 12.191 30355 Z= 0.264 Chirality : 0.037 0.216 3525 Planarity : 0.003 0.046 3608 Dihedral : 12.135 110.219 3880 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.96 % Allowed : 8.92 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.26 (0.17), residues: 2539 helix: 1.41 (0.17), residues: 1025 sheet: -0.89 (0.29), residues: 278 loop : -1.40 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 129 TYR 0.013 0.001 TYR D 135 PHE 0.015 0.001 PHE F 422 TRP 0.014 0.001 TRP E 114 HIS 0.003 0.001 HIS E 33 Details of bonding type rmsd covalent geometry : bond 0.00238 (22072) covalent geometry : angle 0.49691 (30329) hydrogen bonds : bond 0.03986 ( 980) hydrogen bonds : angle 4.36538 ( 2643) metal coordination : bond 0.00567 ( 32) metal coordination : angle 5.18957 ( 26) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue MET 233 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue LYS 524 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.053 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: 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 899 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7237 (mpt) REVERT: B 70 MET cc_start: 0.9213 (ptt) cc_final: 0.8752 (ppp) REVERT: D 48 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8159 (tm-30) REVERT: E 30 CYS cc_start: 0.8576 (t) cc_final: 0.8297 (p) REVERT: E 68 MET cc_start: 0.8640 (tmm) cc_final: 0.8412 (tmm) REVERT: E 106 PHE cc_start: 0.9129 (t80) cc_final: 0.8891 (t80) REVERT: E 182 PHE cc_start: 0.9053 (m-80) cc_final: 0.8662 (m-80) REVERT: E 200 PHE cc_start: 0.8304 (m-10) cc_final: 0.7971 (m-80) REVERT: E 398 TYR cc_start: 0.8755 (m-80) cc_final: 0.8412 (m-80) REVERT: E 574 CYS cc_start: 0.8492 (m) cc_final: 0.6815 (p) REVERT: F 155 ARG cc_start: 0.9346 (mmt180) cc_final: 0.9033 (mmm160) outliers start: 21 outliers final: 17 residues processed: 163 average time/residue: 0.3620 time to fit residues: 92.2945 Evaluate side-chains 168 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 561 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 181 optimal weight: 20.0000 chunk 251 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 HIS A 705 ASN A 822 GLN F 470 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.077966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.052264 restraints weight = 288216.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.054594 restraints weight = 106933.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.056038 restraints weight = 58110.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.056878 restraints weight = 39532.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.057372 restraints weight = 31270.058| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 22104 Z= 0.247 Angle : 0.592 14.309 30355 Z= 0.307 Chirality : 0.038 0.216 3525 Planarity : 0.004 0.044 3608 Dihedral : 12.151 110.979 3880 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.01 % Allowed : 9.14 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.54 (0.17), residues: 2539 helix: 1.19 (0.16), residues: 1025 sheet: -1.00 (0.29), residues: 272 loop : -1.58 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 129 TYR 0.013 0.002 TYR D 135 PHE 0.037 0.002 PHE E 81 TRP 0.018 0.001 TRP E 114 HIS 0.006 0.001 HIS A 752 Details of bonding type rmsd covalent geometry : bond 0.00512 (22072) covalent geometry : angle 0.56453 (30329) hydrogen bonds : bond 0.04312 ( 980) hydrogen bonds : angle 4.67828 ( 2643) metal coordination : bond 0.01207 ( 32) metal coordination : angle 6.07767 ( 26) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue MET 233 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue LYS 524 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.038 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: 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 899 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7318 (mpt) REVERT: B 70 MET cc_start: 0.9203 (ptt) cc_final: 0.8768 (ppp) REVERT: D 48 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8200 (tm-30) REVERT: E 30 CYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8327 (p) REVERT: E 68 MET cc_start: 0.8724 (tmm) cc_final: 0.8485 (tmm) REVERT: E 182 PHE cc_start: 0.9129 (m-80) cc_final: 0.8748 (m-80) REVERT: E 200 PHE cc_start: 0.8401 (m-10) cc_final: 0.8066 (m-80) REVERT: E 574 CYS cc_start: 0.8509 (m) cc_final: 0.6742 (p) REVERT: F 567 ARG cc_start: 0.4930 (mmp80) cc_final: 0.4032 (ptp-170) REVERT: F 576 MET cc_start: 0.0880 (ttp) cc_final: 0.0653 (ttp) outliers start: 22 outliers final: 18 residues processed: 162 average time/residue: 0.2992 time to fit residues: 76.0030 Evaluate side-chains 169 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 561 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 247 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 250 optimal weight: 0.7980 chunk 132 optimal weight: 0.0870 chunk 46 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 234 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.079226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.053495 restraints weight = 283556.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.055900 restraints weight = 104309.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.057409 restraints weight = 56132.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.058261 restraints weight = 37797.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.058782 restraints weight = 29815.942| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22104 Z= 0.116 Angle : 0.532 12.444 30355 Z= 0.270 Chirality : 0.037 0.217 3525 Planarity : 0.003 0.045 3608 Dihedral : 12.167 109.429 3880 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.91 % Allowed : 9.56 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.27 (0.17), residues: 2539 helix: 1.43 (0.17), residues: 1024 sheet: -0.97 (0.29), residues: 279 loop : -1.42 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 332 TYR 0.015 0.001 TYR A 595 PHE 0.013 0.001 PHE F 357 TRP 0.014 0.001 TRP E 114 HIS 0.004 0.001 HIS E 464 Details of bonding type rmsd covalent geometry : bond 0.00250 (22072) covalent geometry : angle 0.50964 (30329) hydrogen bonds : bond 0.03991 ( 980) hydrogen bonds : angle 4.35876 ( 2643) metal coordination : bond 0.00606 ( 32) metal coordination : angle 5.24279 ( 26) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue MET 233 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue LYS 524 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 1.232 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: 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 899 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7242 (mpt) REVERT: B 70 MET cc_start: 0.9152 (ptt) cc_final: 0.8720 (ppp) REVERT: D 48 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8173 (tm-30) REVERT: E 30 CYS cc_start: 0.8602 (t) cc_final: 0.8317 (p) REVERT: E 68 MET cc_start: 0.8730 (tmm) cc_final: 0.8482 (tmm) REVERT: E 182 PHE cc_start: 0.9073 (m-80) cc_final: 0.8681 (m-80) REVERT: E 200 PHE cc_start: 0.8375 (m-10) cc_final: 0.8029 (m-80) REVERT: E 574 CYS cc_start: 0.8475 (m) cc_final: 0.6722 (p) REVERT: F 567 ARG cc_start: 0.4931 (mmp80) cc_final: 0.4169 (ptp-170) outliers start: 20 outliers final: 18 residues processed: 162 average time/residue: 0.3214 time to fit residues: 81.8782 Evaluate side-chains 166 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 274 MET Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 561 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 106 optimal weight: 2.9990 chunk 218 optimal weight: 8.9990 chunk 246 optimal weight: 20.0000 chunk 242 optimal weight: 9.9990 chunk 44 optimal weight: 0.0070 chunk 52 optimal weight: 0.9990 chunk 231 optimal weight: 1.9990 chunk 132 optimal weight: 0.0570 chunk 118 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 203 optimal weight: 7.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 GLN A 657 ASN A 705 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.079175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.053468 restraints weight = 286234.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.055881 restraints weight = 104300.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.057332 restraints weight = 56306.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.058198 restraints weight = 38082.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.058709 restraints weight = 30025.621| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22104 Z= 0.122 Angle : 0.530 12.555 30355 Z= 0.269 Chirality : 0.037 0.217 3525 Planarity : 0.003 0.046 3608 Dihedral : 12.105 109.428 3880 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.91 % Allowed : 9.88 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.20 (0.17), residues: 2539 helix: 1.49 (0.17), residues: 1025 sheet: -0.90 (0.30), residues: 274 loop : -1.38 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 332 TYR 0.010 0.001 TYR E 70 PHE 0.016 0.001 PHE E 81 TRP 0.013 0.001 TRP E 114 HIS 0.002 0.001 HIS E 164 Details of bonding type rmsd covalent geometry : bond 0.00259 (22072) covalent geometry : angle 0.50649 (30329) hydrogen bonds : bond 0.03947 ( 980) hydrogen bonds : angle 4.31426 ( 2643) metal coordination : bond 0.00603 ( 32) metal coordination : angle 5.32129 ( 26) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7023.69 seconds wall clock time: 120 minutes 28.09 seconds (7228.09 seconds total)