Starting phenix.real_space_refine on Sat Mar 7 02:34:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fid_31589/03_2026/7fid_31589.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fid_31589/03_2026/7fid_31589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7fid_31589/03_2026/7fid_31589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fid_31589/03_2026/7fid_31589.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fid_31589/03_2026/7fid_31589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fid_31589/03_2026/7fid_31589.map" } resolution = 2.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 135 5.16 5 C 23328 2.51 5 N 6490 2.21 5 O 7024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36992 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} Chain: "C" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "D" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "E" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} Chain: "F" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "A" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} Chain: "S" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.78, per 1000 atoms: 0.24 Number of scatterers: 36992 At special positions: 0 Unit cell: (197.62, 200.08, 194.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 P 15 15.00 O 7024 8.00 N 6490 7.00 C 23328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.7 seconds 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8732 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 42 sheets defined 46.9% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 30 through 38 Processing helix chain 'B' and resid 117 through 139 removed outlier: 3.848A pdb=" N VAL B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 153 removed outlier: 3.593A pdb=" N VAL B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 168 removed outlier: 3.614A pdb=" N HIS B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 181 removed outlier: 3.589A pdb=" N LYS B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 236 removed outlier: 3.817A pdb=" N LEU B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 254 removed outlier: 4.560A pdb=" N LEU B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 274 Processing helix chain 'B' and resid 282 through 296 removed outlier: 3.530A pdb=" N VAL B 296 " --> pdb=" O TRP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 317 removed outlier: 3.651A pdb=" N GLU B 317 " --> pdb=" O GLN B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 339 removed outlier: 3.519A pdb=" N LYS B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 372 removed outlier: 3.971A pdb=" N SER B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 403 through 412 Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.905A pdb=" N MET B 427 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 4.022A pdb=" N VAL B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 505 through 513 removed outlier: 3.809A pdb=" N LYS B 509 " --> pdb=" O TYR B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 534 Processing helix chain 'B' and resid 540 through 561 Processing helix chain 'B' and resid 573 through 579 removed outlier: 3.895A pdb=" N TYR B 577 " --> pdb=" O ASP B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 645 Processing helix chain 'B' and resid 647 through 652 removed outlier: 3.793A pdb=" N TYR B 651 " --> pdb=" O HIS B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 693 removed outlier: 3.588A pdb=" N MET B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 728 removed outlier: 3.519A pdb=" N LYS B 721 " --> pdb=" O GLY B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 746 removed outlier: 4.365A pdb=" N ALA B 741 " --> pdb=" O ASP B 738 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU B 744 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 746 " --> pdb=" O LEU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 752 Processing helix chain 'B' and resid 761 through 770 removed outlier: 3.892A pdb=" N VAL B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 770 " --> pdb=" O LEU B 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 removed outlier: 3.997A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 136 removed outlier: 4.204A pdb=" N VAL C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 143 removed outlier: 4.008A pdb=" N LYS C 140 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N SER C 141 " --> pdb=" O ASN C 138 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG C 143 " --> pdb=" O LYS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 154 removed outlier: 4.063A pdb=" N ALA C 151 " --> pdb=" O TYR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 168 removed outlier: 3.988A pdb=" N HIS C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.664A pdb=" N LYS C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 237 removed outlier: 3.654A pdb=" N ARG C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 256 Processing helix chain 'C' and resid 259 through 274 Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.937A pdb=" N VAL C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C 296 " --> pdb=" O TRP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.706A pdb=" N THR C 311 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 340 removed outlier: 3.755A pdb=" N GLN C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 372 removed outlier: 3.966A pdb=" N GLY C 365 " --> pdb=" O LYS C 361 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARG C 366 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 367 " --> pdb=" O SER C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.939A pdb=" N VAL C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 450 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 505 through 514 removed outlier: 3.915A pdb=" N LYS C 509 " --> pdb=" O TYR C 505 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER C 514 " --> pdb=" O GLN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 534 Processing helix chain 'C' and resid 542 through 561 Processing helix chain 'C' and resid 573 through 579 removed outlier: 3.721A pdb=" N TYR C 577 " --> pdb=" O ASP C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 646 removed outlier: 3.633A pdb=" N ALA C 646 " --> pdb=" O THR C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 660 removed outlier: 3.526A pdb=" N LYS C 660 " --> pdb=" O ASP C 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 656 through 660' Processing helix chain 'C' and resid 679 through 692 Processing helix chain 'C' and resid 717 through 728 removed outlier: 3.569A pdb=" N LYS C 721 " --> pdb=" O GLY C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 746 removed outlier: 4.637A pdb=" N ALA C 741 " --> pdb=" O ASP C 738 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN C 742 " --> pdb=" O ASN C 739 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 743 " --> pdb=" O GLU C 740 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU C 744 " --> pdb=" O ALA C 741 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU C 745 " --> pdb=" O GLN C 742 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 746 " --> pdb=" O LEU C 743 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 738 through 746' Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 761 through 770 removed outlier: 3.961A pdb=" N VAL C 765 " --> pdb=" O ASP C 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 40 removed outlier: 3.925A pdb=" N ARG D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 139 removed outlier: 3.542A pdb=" N HIS D 139 " --> pdb=" O TYR D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 143 Processing helix chain 'D' and resid 145 through 149 removed outlier: 3.746A pdb=" N GLN D 148 " --> pdb=" O ASP D 145 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 149 " --> pdb=" O ARG D 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 145 through 149' Processing helix chain 'D' and resid 157 through 169 removed outlier: 4.070A pdb=" N LEU D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 182 removed outlier: 3.681A pdb=" N LEU D 182 " --> pdb=" O GLU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 239 removed outlier: 3.504A pdb=" N GLY D 239 " --> pdb=" O LYS D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 256 Processing helix chain 'D' and resid 259 through 276 removed outlier: 3.684A pdb=" N MET D 276 " --> pdb=" O ARG D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 295 removed outlier: 3.571A pdb=" N THR D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 322 through 339 removed outlier: 3.683A pdb=" N LYS D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 372 Processing helix chain 'D' and resid 386 through 390 removed outlier: 3.667A pdb=" N GLU D 389 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 412 Processing helix chain 'D' and resid 423 through 427 removed outlier: 3.798A pdb=" N MET D 427 " --> pdb=" O ILE D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 440 removed outlier: 4.209A pdb=" N ALA D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 505 through 514 removed outlier: 3.732A pdb=" N LYS D 509 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER D 514 " --> pdb=" O GLN D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.959A pdb=" N THR D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 561 Processing helix chain 'D' and resid 574 through 579 Processing helix chain 'D' and resid 630 through 646 removed outlier: 3.587A pdb=" N ALA D 646 " --> pdb=" O THR D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 652 removed outlier: 3.983A pdb=" N TYR D 651 " --> pdb=" O HIS D 647 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY D 652 " --> pdb=" O THR D 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 647 through 652' Processing helix chain 'D' and resid 656 through 660 removed outlier: 3.608A pdb=" N LYS D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 656 through 660' Processing helix chain 'D' and resid 679 through 693 Processing helix chain 'D' and resid 717 through 728 removed outlier: 3.797A pdb=" N LYS D 721 " --> pdb=" O GLY D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 745 removed outlier: 4.453A pdb=" N ALA D 741 " --> pdb=" O ASP D 738 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU D 744 " --> pdb=" O ALA D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 752 Processing helix chain 'D' and resid 761 through 770 removed outlier: 3.893A pdb=" N VAL D 765 " --> pdb=" O ASP D 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 39 Processing helix chain 'E' and resid 117 through 137 removed outlier: 4.233A pdb=" N VAL E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 removed outlier: 4.345A pdb=" N SER E 141 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU E 142 " --> pdb=" O HIS E 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 142' Processing helix chain 'E' and resid 157 through 167 Processing helix chain 'E' and resid 172 through 181 Processing helix chain 'E' and resid 185 through 238 Processing helix chain 'E' and resid 247 through 251 removed outlier: 3.878A pdb=" N ARG E 250 " --> pdb=" O GLU E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 271 Processing helix chain 'E' and resid 282 through 295 removed outlier: 3.699A pdb=" N ALA E 286 " --> pdb=" O GLU E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 319 removed outlier: 3.702A pdb=" N GLU E 317 " --> pdb=" O GLN E 313 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS E 319 " --> pdb=" O LEU E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 339 Processing helix chain 'E' and resid 361 through 372 Processing helix chain 'E' and resid 403 through 412 Processing helix chain 'E' and resid 435 through 444 removed outlier: 3.793A pdb=" N VAL E 442 " --> pdb=" O ALA E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 483 Processing helix chain 'E' and resid 494 through 505 Processing helix chain 'E' and resid 506 through 514 Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.722A pdb=" N THR E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 561 Processing helix chain 'E' and resid 573 through 579 Processing helix chain 'E' and resid 630 through 647 removed outlier: 3.504A pdb=" N HIS E 647 " --> pdb=" O TYR E 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 652 removed outlier: 4.158A pdb=" N TYR E 651 " --> pdb=" O HIS E 647 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY E 652 " --> pdb=" O THR E 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 647 through 652' Processing helix chain 'E' and resid 679 through 693 removed outlier: 3.544A pdb=" N MET E 683 " --> pdb=" O ALA E 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 717 through 728 removed outlier: 3.882A pdb=" N LYS E 721 " --> pdb=" O GLY E 717 " (cutoff:3.500A) Processing helix chain 'E' and resid 738 through 746 removed outlier: 5.215A pdb=" N ALA E 741 " --> pdb=" O ASP E 738 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU E 743 " --> pdb=" O GLU E 740 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU E 744 " --> pdb=" O ALA E 741 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU E 745 " --> pdb=" O GLN E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 754 Processing helix chain 'E' and resid 761 through 770 removed outlier: 3.814A pdb=" N VAL E 765 " --> pdb=" O ASP E 761 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU E 770 " --> pdb=" O LEU E 766 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 38 removed outlier: 3.843A pdb=" N ALA F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 136 Processing helix chain 'F' and resid 139 through 143 Processing helix chain 'F' and resid 157 through 167 removed outlier: 3.641A pdb=" N LEU F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 181 Processing helix chain 'F' and resid 185 through 237 Processing helix chain 'F' and resid 246 through 254 removed outlier: 4.042A pdb=" N GLU F 254 " --> pdb=" O ARG F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 267 Processing helix chain 'F' and resid 284 through 294 removed outlier: 3.749A pdb=" N THR F 288 " --> pdb=" O THR F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 319 removed outlier: 3.570A pdb=" N THR F 311 " --> pdb=" O ASP F 307 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU F 317 " --> pdb=" O GLN F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 339 Processing helix chain 'F' and resid 361 through 372 Processing helix chain 'F' and resid 386 through 390 Processing helix chain 'F' and resid 403 through 412 removed outlier: 3.587A pdb=" N VAL F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 427 Processing helix chain 'F' and resid 435 through 444 Processing helix chain 'F' and resid 447 through 451 Processing helix chain 'F' and resid 478 through 483 removed outlier: 3.771A pdb=" N ASP F 483 " --> pdb=" O ARG F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 513 Proline residue: F 508 - end of helix Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.558A pdb=" N LEU F 528 " --> pdb=" O ASP F 524 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR F 535 " --> pdb=" O ILE F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 559 removed outlier: 3.531A pdb=" N ILE F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU F 559 " --> pdb=" O ALA F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 578 removed outlier: 3.868A pdb=" N TYR F 577 " --> pdb=" O ASP F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 647 Processing helix chain 'F' and resid 676 through 678 No H-bonds generated for 'chain 'F' and resid 676 through 678' Processing helix chain 'F' and resid 679 through 693 Processing helix chain 'F' and resid 717 through 727 removed outlier: 3.811A pdb=" N LYS F 721 " --> pdb=" O GLY F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 744 removed outlier: 4.640A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU F 743 " --> pdb=" O GLU F 740 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU F 744 " --> pdb=" O ALA F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 752 Processing helix chain 'F' and resid 761 through 770 removed outlier: 3.869A pdb=" N VAL F 765 " --> pdb=" O ASP F 761 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU F 770 " --> pdb=" O LEU F 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 37 removed outlier: 3.761A pdb=" N VAL A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 58 through 62 removed outlier: 3.779A pdb=" N ASP A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 62 " --> pdb=" O PRO A 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 58 through 62' Processing helix chain 'A' and resid 117 through 136 removed outlier: 4.063A pdb=" N VAL A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 168 removed outlier: 3.763A pdb=" N HIS A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 removed outlier: 3.874A pdb=" N LYS A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 238 removed outlier: 3.701A pdb=" N ARG A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.696A pdb=" N VAL A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 271 removed outlier: 3.584A pdb=" N ASP A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 294 removed outlier: 4.268A pdb=" N THR A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.860A pdb=" N THR A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 339 removed outlier: 4.066A pdb=" N ARG A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 339 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 removed outlier: 4.177A pdb=" N SER A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 412 Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.820A pdb=" N LYS A 426 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET A 427 " --> pdb=" O ILE A 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 423 through 427' Processing helix chain 'A' and resid 434 through 443 removed outlier: 3.882A pdb=" N ALA A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 removed outlier: 3.918A pdb=" N PHE A 451 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.722A pdb=" N ASP A 483 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 513 removed outlier: 5.041A pdb=" N TRP A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Proline residue: A 508 - end of helix Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.786A pdb=" N THR A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 561 Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.894A pdb=" N TYR A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 647 Processing helix chain 'A' and resid 656 through 659 removed outlier: 3.827A pdb=" N ASN A 659 " --> pdb=" O ASP A 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 656 through 659' Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 717 through 728 removed outlier: 3.543A pdb=" N LYS A 721 " --> pdb=" O GLY A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 removed outlier: 4.878A pdb=" N ALA A 741 " --> pdb=" O ASP A 738 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 743 " --> pdb=" O GLU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 770 removed outlier: 3.798A pdb=" N VAL A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 8 through 9 removed outlier: 6.499A pdb=" N ILE B 8 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 20 through 25 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.858A pdb=" N ASP B 96 " --> pdb=" O ARG B 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 376 through 380 removed outlier: 6.392A pdb=" N LEU B 351 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA B 471 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU B 353 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE B 350 " --> pdb=" O GLU B 486 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE B 488 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL B 352 " --> pdb=" O ILE B 488 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522 removed outlier: 6.915A pdb=" N GLU B 521 " --> pdb=" O ILE B 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 596 through 602 removed outlier: 5.902A pdb=" N LYS B 622 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL B 665 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER B 624 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.878A pdb=" N ALA B 701 " --> pdb=" O VAL B 734 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE B 733 " --> pdb=" O LYS B 757 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL B 759 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 735 " --> pdb=" O VAL B 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 705 through 706 Processing sheet with id=AA9, first strand: chain 'C' and resid 7 through 8 Processing sheet with id=AB1, first strand: chain 'C' and resid 20 through 23 removed outlier: 6.767A pdb=" N GLU C 87 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL C 71 " --> pdb=" O GLU C 87 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARG C 89 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ALA C 69 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG C 91 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL C 67 " --> pdb=" O ARG C 91 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLN C 93 " --> pdb=" O TRP C 65 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TRP C 65 " --> pdb=" O GLN C 93 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 376 through 380 removed outlier: 6.164A pdb=" N ILE C 419 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N THR C 470 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU C 421 " --> pdb=" O THR C 470 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU C 351 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ALA C 471 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU C 353 " --> pdb=" O ALA C 471 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 452 Processing sheet with id=AB4, first strand: chain 'C' and resid 521 through 522 removed outlier: 6.614A pdb=" N GLU C 521 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 596 through 603 removed outlier: 5.965A pdb=" N LYS C 622 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL C 665 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 700 through 702 removed outlier: 6.698A pdb=" N ALA C 701 " --> pdb=" O VAL C 734 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 705 through 706 Processing sheet with id=AB8, first strand: chain 'D' and resid 21 through 23 removed outlier: 4.304A pdb=" N THR D 21 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL D 86 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLU D 87 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL D 71 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG D 89 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ALA D 69 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG D 91 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL D 67 " --> pdb=" O ARG D 91 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN D 93 " --> pdb=" O TRP D 65 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP D 65 " --> pdb=" O GLN D 93 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N TRP D 65 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ALA D 48 " --> pdb=" O TRP D 65 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE D 45 " --> pdb=" O PRO D 6 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL D 47 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG D 104 " --> pdb=" O ILE D 98 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 376 through 380 removed outlier: 3.632A pdb=" N THR D 470 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 451 through 452 Processing sheet with id=AC2, first strand: chain 'D' and resid 521 through 522 removed outlier: 6.996A pdb=" N GLU D 521 " --> pdb=" O ILE D 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 596 through 603 removed outlier: 3.911A pdb=" N LYS D 622 " --> pdb=" O VAL D 661 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 701 through 702 Processing sheet with id=AC5, first strand: chain 'D' and resid 705 through 706 Processing sheet with id=AC6, first strand: chain 'E' and resid 7 through 9 removed outlier: 3.509A pdb=" N VAL E 47 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL E 71 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLU E 87 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN E 73 " --> pdb=" O MET E 85 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET E 75 " --> pdb=" O GLN E 83 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLN E 83 " --> pdb=" O MET E 75 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 418 through 421 removed outlier: 5.869A pdb=" N ILE E 419 " --> pdb=" O ILE E 468 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N THR E 470 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU E 421 " --> pdb=" O THR E 470 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU E 351 " --> pdb=" O PHE E 467 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.754A pdb=" N GLU E 521 " --> pdb=" O ILE E 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 596 through 603 removed outlier: 6.572A pdb=" N SER E 624 " --> pdb=" O VAL E 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 700 through 702 removed outlier: 6.375A pdb=" N ILE E 733 " --> pdb=" O LYS E 757 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL E 759 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU E 735 " --> pdb=" O VAL E 759 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 705 through 706 removed outlier: 3.562A pdb=" N MET E 713 " --> pdb=" O GLU E 705 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 8 through 10 removed outlier: 3.903A pdb=" N ILE F 8 " --> pdb=" O PHE F 45 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL F 47 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU F 10 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY F 66 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA F 90 " --> pdb=" O GLN F 68 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL F 70 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ALA F 88 " --> pdb=" O VAL F 70 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 21 through 25 Processing sheet with id=AD5, first strand: chain 'F' and resid 376 through 380 removed outlier: 6.052A pdb=" N LEU F 351 " --> pdb=" O THR F 469 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA F 471 " --> pdb=" O LEU F 351 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU F 353 " --> pdb=" O ALA F 471 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE F 350 " --> pdb=" O GLU F 486 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE F 488 " --> pdb=" O ILE F 350 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL F 352 " --> pdb=" O ILE F 488 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 520 through 522 removed outlier: 6.707A pdb=" N GLU F 521 " --> pdb=" O ILE F 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'F' and resid 596 through 603 Processing sheet with id=AD8, first strand: chain 'F' and resid 701 through 702 removed outlier: 6.862A pdb=" N ALA F 701 " --> pdb=" O VAL F 734 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 705 through 706 removed outlier: 3.510A pdb=" N GLU F 705 " --> pdb=" O MET F 713 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 4 through 6 removed outlier: 3.675A pdb=" N ARG A 106 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP A 96 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 22 through 25 removed outlier: 6.520A pdb=" N GLN A 83 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA A 74 " --> pdb=" O GLN A 83 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N MET A 85 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLN A 68 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG A 91 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY A 66 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 376 through 379 removed outlier: 6.312A pdb=" N LEU A 351 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ALA A 471 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU A 353 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL A 352 " --> pdb=" O ILE A 488 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.773A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'A' and resid 596 through 603 removed outlier: 5.979A pdb=" N LYS A 622 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL A 665 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N SER A 624 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.946A pdb=" N ALA A 701 " --> pdb=" O VAL A 734 " (cutoff:3.500A) 1593 hydrogen bonds defined for protein. 4620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.25 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 12595 1.35 - 1.50: 10662 1.50 - 1.65: 14145 1.65 - 1.80: 211 1.80 - 1.95: 56 Bond restraints: 37669 Sorted by residual: bond pdb=" C ILE F 113 " pdb=" N PHE F 114 " ideal model delta sigma weight residual 1.329 1.390 -0.061 1.35e-02 5.49e+03 2.05e+01 bond pdb=" C ASP A 51 " pdb=" N PRO A 52 " ideal model delta sigma weight residual 1.331 1.382 -0.051 1.21e-02 6.83e+03 1.75e+01 bond pdb=" CA GLU A 247 " pdb=" C GLU A 247 " ideal model delta sigma weight residual 1.522 1.469 0.053 1.40e-02 5.10e+03 1.45e+01 bond pdb=" N SER E 380 " pdb=" CA SER E 380 " ideal model delta sigma weight residual 1.461 1.510 -0.049 1.41e-02 5.03e+03 1.22e+01 bond pdb=" C ASP B 51 " pdb=" N PRO B 52 " ideal model delta sigma weight residual 1.334 1.404 -0.071 2.34e-02 1.83e+03 9.10e+00 ... (remaining 37664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.98: 50948 5.98 - 11.97: 145 11.97 - 17.95: 12 17.95 - 23.93: 0 23.93 - 29.91: 1 Bond angle restraints: 51106 Sorted by residual: angle pdb=" CA LEU D 161 " pdb=" CB LEU D 161 " pdb=" CG LEU D 161 " ideal model delta sigma weight residual 116.30 146.21 -29.91 3.50e+00 8.16e-02 7.30e+01 angle pdb=" CB ARG D 328 " pdb=" CG ARG D 328 " pdb=" CD ARG D 328 " ideal model delta sigma weight residual 111.30 126.45 -15.15 2.30e+00 1.89e-01 4.34e+01 angle pdb=" N GLY D 242 " pdb=" CA GLY D 242 " pdb=" C GLY D 242 " ideal model delta sigma weight residual 115.32 108.02 7.30 1.31e+00 5.83e-01 3.10e+01 angle pdb=" N PRO F 52 " pdb=" CA PRO F 52 " pdb=" C PRO F 52 " ideal model delta sigma weight residual 111.15 119.44 -8.29 1.58e+00 4.01e-01 2.75e+01 angle pdb=" CA ARG B 395 " pdb=" CB ARG B 395 " pdb=" CG ARG B 395 " ideal model delta sigma weight residual 114.10 124.57 -10.47 2.00e+00 2.50e-01 2.74e+01 ... (remaining 51101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.32: 22976 33.32 - 66.64: 249 66.64 - 99.96: 30 99.96 - 133.28: 7 133.28 - 166.60: 2 Dihedral angle restraints: 23264 sinusoidal: 9705 harmonic: 13559 Sorted by residual: dihedral pdb=" CA ASP D 51 " pdb=" C ASP D 51 " pdb=" N PRO D 52 " pdb=" CA PRO D 52 " ideal model delta harmonic sigma weight residual -180.00 -117.34 -62.66 0 5.00e+00 4.00e-02 1.57e+02 dihedral pdb=" CA ASP C 51 " pdb=" C ASP C 51 " pdb=" N PRO C 52 " pdb=" CA PRO C 52 " ideal model delta harmonic sigma weight residual -180.00 -119.70 -60.30 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA GLU D 304 " pdb=" C GLU D 304 " pdb=" N VAL D 305 " pdb=" CA VAL D 305 " ideal model delta harmonic sigma weight residual -180.00 -126.73 -53.27 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 23261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4959 0.088 - 0.176: 810 0.176 - 0.263: 56 0.263 - 0.351: 3 0.351 - 0.439: 2 Chirality restraints: 5830 Sorted by residual: chirality pdb=" CG LEU D 161 " pdb=" CB LEU D 161 " pdb=" CD1 LEU D 161 " pdb=" CD2 LEU D 161 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CG LEU E 270 " pdb=" CB LEU E 270 " pdb=" CD1 LEU E 270 " pdb=" CD2 LEU E 270 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CB ILE B 398 " pdb=" CA ILE B 398 " pdb=" CG1 ILE B 398 " pdb=" CG2 ILE B 398 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 5827 not shown) Planarity restraints: 6627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 404 " 0.031 2.00e-02 2.50e+03 6.00e-02 3.60e+01 pdb=" C LYS E 404 " -0.104 2.00e-02 2.50e+03 pdb=" O LYS E 404 " 0.039 2.00e-02 2.50e+03 pdb=" N LEU E 405 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 379 " 0.027 2.00e-02 2.50e+03 5.27e-02 2.77e+01 pdb=" C ILE E 379 " -0.091 2.00e-02 2.50e+03 pdb=" O ILE E 379 " 0.034 2.00e-02 2.50e+03 pdb=" N SER E 380 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 247 " 0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C GLU A 247 " -0.076 2.00e-02 2.50e+03 pdb=" O GLU A 247 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA A 248 " 0.026 2.00e-02 2.50e+03 ... (remaining 6624 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1725 2.71 - 3.26: 33666 3.26 - 3.81: 57195 3.81 - 4.35: 69865 4.35 - 4.90: 119408 Nonbonded interactions: 281859 Sorted by model distance: nonbonded pdb=" O ASP A 422 " pdb=" OG1 THR A 470 " model vdw 2.165 3.040 nonbonded pdb=" O VAL A 359 " pdb=" O2B AGS A 901 " model vdw 2.191 3.040 nonbonded pdb=" O1B AGS A 901 " pdb=" O3G AGS A 901 " model vdw 2.220 3.040 nonbonded pdb=" O1B AGS C 901 " pdb=" O2G AGS C 901 " model vdw 2.235 3.040 nonbonded pdb=" O VAL C 359 " pdb=" O2B AGS C 901 " model vdw 2.239 3.040 ... (remaining 281854 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 'A' and resid 2 through 780) selection = (chain 'B' and resid 2 through 780) selection = (chain 'C' and resid 2 through 780) selection = (chain 'D' and resid 2 through 780) selection = (chain 'E' and resid 2 through 780) selection = (chain 'F' and resid 2 through 780) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 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: 0.060 Extract box with map and model: 0.870 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 34.850 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 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:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.010 0.126 37669 Z= 0.401 Angle : 1.103 29.913 51106 Z= 0.592 Chirality : 0.063 0.439 5830 Planarity : 0.008 0.086 6627 Dihedral : 11.369 166.601 14532 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.71 % Favored : 94.12 % Rotamer: Outliers : 0.36 % Allowed : 4.20 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.56 (0.10), residues: 4662 helix: -2.36 (0.09), residues: 1984 sheet: -0.54 (0.21), residues: 582 loop : -2.87 (0.11), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG E 519 TYR 0.041 0.003 TYR F 135 PHE 0.032 0.003 PHE D 132 TRP 0.027 0.003 TRP C 602 HIS 0.022 0.002 HIS D 168 Details of bonding type rmsd covalent geometry : bond 0.00954 (37669) covalent geometry : angle 1.10266 (51106) hydrogen bonds : bond 0.16249 ( 1593) hydrogen bonds : angle 6.61571 ( 4620) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 348 time to evaluate : 1.393 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: B 85 MET cc_start: 0.1062 (tpp) cc_final: -0.0136 (ppp) REVERT: D 38 MET cc_start: 0.3760 (mtt) cc_final: 0.3355 (mpm) REVERT: D 160 MET cc_start: 0.4155 (tpt) cc_final: 0.2581 (ptm) REVERT: E 75 MET cc_start: 0.0959 (ttp) cc_final: 0.0111 (ttp) REVERT: E 373 ASN cc_start: 0.8498 (m110) cc_final: 0.8229 (m110) REVERT: F 342 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6724 (tm) outliers start: 14 outliers final: 4 residues processed: 361 average time/residue: 1.0050 time to fit residues: 417.6533 Evaluate side-chains 232 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 227 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain F residue 342 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 50.0000 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 50.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 HIS B 319 HIS ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 ASN D 139 HIS D 168 HIS D 211 GLN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN D 393 HIS D 407 HIS E 18 HIS E 216 GLN E 220 ASN E 234 GLN E 277 GLN E 319 HIS ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 647 HIS A 68 GLN A 319 HIS A 447 GLN A 472 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.186646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.110114 restraints weight = 66997.813| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.98 r_work: 0.2874 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37669 Z= 0.125 Angle : 0.672 15.909 51106 Z= 0.336 Chirality : 0.044 0.173 5830 Planarity : 0.006 0.069 6627 Dihedral : 8.745 163.028 5262 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.14 % Favored : 95.84 % Rotamer: Outliers : 1.60 % Allowed : 7.61 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.11), residues: 4662 helix: -0.50 (0.11), residues: 2027 sheet: -0.30 (0.20), residues: 599 loop : -2.40 (0.12), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 479 TYR 0.026 0.001 TYR D 167 PHE 0.029 0.001 PHE B 203 TRP 0.023 0.002 TRP F 292 HIS 0.007 0.001 HIS D 168 Details of bonding type rmsd covalent geometry : bond 0.00269 (37669) covalent geometry : angle 0.67224 (51106) hydrogen bonds : bond 0.04323 ( 1593) hydrogen bonds : angle 4.89656 ( 4620) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 250 time to evaluate : 1.419 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: B 85 MET cc_start: 0.1499 (tpp) cc_final: 0.0735 (ppp) REVERT: B 479 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7813 (mpt180) REVERT: B 713 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8405 (mtp) REVERT: C 230 MET cc_start: 0.7983 (ppp) cc_final: 0.7539 (pmm) REVERT: C 258 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7744 (ptm) REVERT: C 323 LYS cc_start: 0.8597 (mmmm) cc_final: 0.8332 (mmpt) REVERT: C 594 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8678 (t) REVERT: C 702 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8987 (ptp) REVERT: D 38 MET cc_start: 0.3896 (mtt) cc_final: 0.3539 (mpm) REVERT: D 160 MET cc_start: 0.2603 (tpt) cc_final: 0.2308 (ptm) REVERT: D 423 GLU cc_start: 0.8520 (mp0) cc_final: 0.8190 (mt-10) REVERT: D 432 ARG cc_start: 0.8181 (tpp80) cc_final: 0.7971 (ttt-90) REVERT: D 479 ARG cc_start: 0.8100 (mmm160) cc_final: 0.7723 (mmm160) REVERT: D 546 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7803 (mp0) REVERT: F 50 ARG cc_start: 0.3311 (OUTLIER) cc_final: 0.3031 (mpt90) REVERT: F 258 MET cc_start: 0.5305 (mmt) cc_final: 0.5041 (mmt) REVERT: F 372 MET cc_start: 0.8653 (mtp) cc_final: 0.8446 (mtp) REVERT: F 455 TYR cc_start: 0.7657 (t80) cc_final: 0.7403 (t80) REVERT: F 713 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8522 (mpp) REVERT: A 217 MET cc_start: 0.4829 (mmm) cc_final: 0.4569 (mmm) REVERT: A 391 ARG cc_start: 0.7669 (mtm-85) cc_final: 0.7469 (mtt-85) REVERT: A 485 MET cc_start: 0.9086 (mtt) cc_final: 0.8794 (mtp) REVERT: A 748 LYS cc_start: 0.9255 (mtpp) cc_final: 0.8912 (mmtt) outliers start: 63 outliers final: 12 residues processed: 299 average time/residue: 0.8666 time to fit residues: 304.4959 Evaluate side-chains 244 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 713 MET Chi-restraints excluded: chain A residue 256 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 367 optimal weight: 4.9990 chunk 193 optimal weight: 10.0000 chunk 354 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 chunk 238 optimal weight: 5.9990 chunk 356 optimal weight: 0.9980 chunk 258 optimal weight: 0.5980 chunk 39 optimal weight: 8.9990 chunk 316 optimal weight: 40.0000 chunk 128 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 ASN D 177 GLN D 220 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS E 377 HIS ** E 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 447 GLN ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.183926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107276 restraints weight = 66365.090| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 4.46 r_work: 0.2789 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 37669 Z= 0.230 Angle : 0.703 14.606 51106 Z= 0.348 Chirality : 0.047 0.175 5830 Planarity : 0.005 0.071 6627 Dihedral : 8.417 160.189 5261 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.22 % Rotamer: Outliers : 1.91 % Allowed : 9.08 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.12), residues: 4662 helix: 0.27 (0.12), residues: 2027 sheet: -0.09 (0.21), residues: 611 loop : -2.17 (0.12), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 222 TYR 0.025 0.002 TYR D 167 PHE 0.032 0.002 PHE B 466 TRP 0.021 0.001 TRP E 292 HIS 0.014 0.001 HIS E 407 Details of bonding type rmsd covalent geometry : bond 0.00558 (37669) covalent geometry : angle 0.70312 (51106) hydrogen bonds : bond 0.04901 ( 1593) hydrogen bonds : angle 4.73026 ( 4620) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 232 time to evaluate : 1.345 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: B 85 MET cc_start: 0.1503 (tpp) cc_final: 0.0735 (ppp) REVERT: B 160 MET cc_start: 0.4294 (tpt) cc_final: 0.3873 (mpt) REVERT: B 230 MET cc_start: 0.6640 (mmt) cc_final: 0.6432 (mpm) REVERT: B 713 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8496 (mtt) REVERT: C 230 MET cc_start: 0.8077 (ppp) cc_final: 0.7413 (pmm) REVERT: C 323 LYS cc_start: 0.8713 (mmmm) cc_final: 0.8435 (mmpt) REVERT: C 631 GLU cc_start: 0.8302 (mp0) cc_final: 0.7906 (mm-30) REVERT: D 85 MET cc_start: 0.4204 (tpt) cc_final: 0.3791 (pmm) REVERT: D 160 MET cc_start: 0.2451 (tpt) cc_final: 0.2166 (ptm) REVERT: D 423 GLU cc_start: 0.8555 (mp0) cc_final: 0.8320 (mt-10) REVERT: E 407 HIS cc_start: 0.7763 (OUTLIER) cc_final: 0.7218 (p-80) REVERT: E 439 MET cc_start: 0.8928 (mmm) cc_final: 0.8366 (ptt) REVERT: E 476 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8265 (p) REVERT: F 50 ARG cc_start: 0.3606 (OUTLIER) cc_final: 0.3357 (mpt90) REVERT: F 258 MET cc_start: 0.5131 (mmt) cc_final: 0.4860 (mmt) REVERT: F 713 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8523 (mtm) REVERT: A 246 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8742 (pp) REVERT: A 247 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8844 (mp0) REVERT: A 276 MET cc_start: 0.7363 (tpp) cc_final: 0.6948 (tpp) REVERT: A 308 ILE cc_start: 0.8469 (pp) cc_final: 0.8068 (mt) REVERT: A 485 MET cc_start: 0.9110 (mtt) cc_final: 0.8808 (mtp) outliers start: 75 outliers final: 30 residues processed: 287 average time/residue: 0.8206 time to fit residues: 279.0157 Evaluate side-chains 257 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 407 HIS Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 713 MET Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 294 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 326 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 chunk 378 optimal weight: 1.9990 chunk 161 optimal weight: 20.0000 chunk 218 optimal weight: 4.9990 chunk 398 optimal weight: 50.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 ASN D 229 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 HIS E 377 HIS ** E 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.184207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.107625 restraints weight = 66416.772| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 4.43 r_work: 0.2785 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 37669 Z= 0.163 Angle : 0.656 15.631 51106 Z= 0.320 Chirality : 0.045 0.192 5830 Planarity : 0.005 0.070 6627 Dihedral : 8.225 159.317 5261 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.29 % Favored : 95.69 % Rotamer: Outliers : 2.32 % Allowed : 9.39 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.12), residues: 4662 helix: 0.73 (0.12), residues: 2016 sheet: -0.02 (0.20), residues: 644 loop : -2.04 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 479 TYR 0.023 0.001 TYR D 167 PHE 0.027 0.001 PHE B 203 TRP 0.019 0.001 TRP E 292 HIS 0.014 0.001 HIS E 407 Details of bonding type rmsd covalent geometry : bond 0.00389 (37669) covalent geometry : angle 0.65617 (51106) hydrogen bonds : bond 0.04126 ( 1593) hydrogen bonds : angle 4.51348 ( 4620) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 241 time to evaluate : 1.419 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: B 85 MET cc_start: 0.1507 (tpp) cc_final: 0.0747 (ppp) REVERT: B 160 MET cc_start: 0.4223 (tpt) cc_final: 0.3890 (mpt) REVERT: B 479 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8227 (mpt180) REVERT: C 230 MET cc_start: 0.8169 (ppp) cc_final: 0.7811 (ppp) REVERT: C 323 LYS cc_start: 0.8627 (mmmm) cc_final: 0.8351 (mmpt) REVERT: C 591 GLU cc_start: 0.8718 (pm20) cc_final: 0.8388 (pm20) REVERT: C 594 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8765 (t) REVERT: D 85 MET cc_start: 0.4272 (tpt) cc_final: 0.3899 (pmm) REVERT: D 276 MET cc_start: 0.8699 (ptp) cc_final: 0.8478 (ptm) REVERT: D 423 GLU cc_start: 0.8590 (mp0) cc_final: 0.8366 (mt-10) REVERT: D 432 ARG cc_start: 0.8438 (ttt-90) cc_final: 0.8218 (ttt180) REVERT: E 407 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.7263 (p-80) REVERT: E 439 MET cc_start: 0.8823 (mmm) cc_final: 0.8297 (ptt) REVERT: E 476 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8244 (p) REVERT: F 229 GLN cc_start: 0.9016 (pp30) cc_final: 0.8664 (pp30) REVERT: F 258 MET cc_start: 0.5152 (mmt) cc_final: 0.4883 (mmt) REVERT: F 290 LEU cc_start: 0.8940 (mm) cc_final: 0.8730 (tm) REVERT: F 389 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7666 (mp0) REVERT: F 713 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8520 (mtm) REVERT: A 247 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8853 (mp0) REVERT: A 276 MET cc_start: 0.7335 (tpp) cc_final: 0.6798 (tpp) REVERT: A 308 ILE cc_start: 0.8441 (pp) cc_final: 0.8065 (mt) REVERT: A 485 MET cc_start: 0.9106 (mtt) cc_final: 0.8901 (mtp) REVERT: A 748 LYS cc_start: 0.9249 (mtpp) cc_final: 0.8985 (mptt) outliers start: 91 outliers final: 39 residues processed: 304 average time/residue: 0.8372 time to fit residues: 302.1237 Evaluate side-chains 269 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 224 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 407 HIS Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain F residue 713 MET Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 323 optimal weight: 6.9990 chunk 372 optimal weight: 4.9990 chunk 172 optimal weight: 40.0000 chunk 328 optimal weight: 9.9990 chunk 15 optimal weight: 50.0000 chunk 262 optimal weight: 4.9990 chunk 342 optimal weight: 9.9990 chunk 425 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 259 optimal weight: 30.0000 chunk 361 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 ASN D 229 GLN D 472 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.182069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.104226 restraints weight = 66440.579| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 4.48 r_work: 0.2774 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 37669 Z= 0.294 Angle : 0.722 17.194 51106 Z= 0.355 Chirality : 0.048 0.211 5830 Planarity : 0.005 0.073 6627 Dihedral : 8.218 158.852 5261 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.87 % Favored : 95.09 % Rotamer: Outliers : 2.65 % Allowed : 10.05 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.12), residues: 4662 helix: 0.80 (0.12), residues: 2039 sheet: 0.02 (0.20), residues: 655 loop : -2.03 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 536 TYR 0.031 0.002 TYR A 332 PHE 0.029 0.002 PHE B 466 TRP 0.021 0.001 TRP E 292 HIS 0.014 0.001 HIS E 407 Details of bonding type rmsd covalent geometry : bond 0.00717 (37669) covalent geometry : angle 0.72197 (51106) hydrogen bonds : bond 0.04995 ( 1593) hydrogen bonds : angle 4.58529 ( 4620) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 228 time to evaluate : 1.466 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: B 85 MET cc_start: 0.1512 (tpp) cc_final: 0.0746 (ppp) REVERT: B 479 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8371 (mpt180) REVERT: C 323 LYS cc_start: 0.8777 (mmmm) cc_final: 0.8498 (mmtt) REVERT: C 631 GLU cc_start: 0.8390 (mp0) cc_final: 0.7976 (mm-30) REVERT: D 85 MET cc_start: 0.4178 (tpt) cc_final: 0.3777 (pmm) REVERT: D 276 MET cc_start: 0.8786 (ptp) cc_final: 0.8376 (ptm) REVERT: E 407 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7306 (p-80) REVERT: E 439 MET cc_start: 0.8823 (mmm) cc_final: 0.8288 (ptt) REVERT: E 476 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8312 (p) REVERT: F 217 MET cc_start: 0.8054 (mmp) cc_final: 0.7711 (mmp) REVERT: F 290 LEU cc_start: 0.8967 (mm) cc_final: 0.8692 (tm) REVERT: F 372 MET cc_start: 0.8787 (mtp) cc_final: 0.8565 (ttp) REVERT: A 85 MET cc_start: 0.1507 (mpp) cc_final: 0.1054 (mpp) REVERT: A 247 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.8899 (mp0) REVERT: A 276 MET cc_start: 0.7394 (tpp) cc_final: 0.6833 (tpp) REVERT: A 308 ILE cc_start: 0.8528 (pp) cc_final: 0.8226 (mp) REVERT: A 485 MET cc_start: 0.9170 (mtt) cc_final: 0.8869 (mtp) outliers start: 104 outliers final: 49 residues processed: 308 average time/residue: 0.7755 time to fit residues: 283.9339 Evaluate side-chains 272 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 219 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 407 HIS Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 682 THR Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 489 GLU Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain F residue 552 ARG Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 329 optimal weight: 9.9990 chunk 270 optimal weight: 40.0000 chunk 40 optimal weight: 0.9990 chunk 245 optimal weight: 50.0000 chunk 293 optimal weight: 7.9990 chunk 365 optimal weight: 3.9990 chunk 5 optimal weight: 40.0000 chunk 57 optimal weight: 0.5980 chunk 296 optimal weight: 3.9990 chunk 451 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 GLN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.183052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.105601 restraints weight = 66413.306| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 4.34 r_work: 0.2814 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 37669 Z= 0.171 Angle : 0.659 16.092 51106 Z= 0.322 Chirality : 0.045 0.234 5830 Planarity : 0.005 0.072 6627 Dihedral : 8.106 158.805 5261 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.16 % Allowed : 11.15 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.12), residues: 4662 helix: 1.09 (0.12), residues: 2018 sheet: 0.10 (0.21), residues: 649 loop : -1.91 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 385 TYR 0.025 0.001 TYR A 332 PHE 0.026 0.001 PHE B 203 TRP 0.020 0.001 TRP E 292 HIS 0.015 0.001 HIS E 407 Details of bonding type rmsd covalent geometry : bond 0.00410 (37669) covalent geometry : angle 0.65863 (51106) hydrogen bonds : bond 0.04114 ( 1593) hydrogen bonds : angle 4.37825 ( 4620) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 229 time to evaluate : 1.507 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: B 85 MET cc_start: 0.1528 (tpp) cc_final: 0.0714 (ppp) REVERT: B 479 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8279 (mpt180) REVERT: C 230 MET cc_start: 0.7140 (ppp) cc_final: 0.6726 (pmm) REVERT: C 323 LYS cc_start: 0.8708 (mmmm) cc_final: 0.8446 (mmpt) REVERT: D 85 MET cc_start: 0.4209 (tpt) cc_final: 0.3814 (pmm) REVERT: D 432 ARG cc_start: 0.8636 (ttt180) cc_final: 0.8343 (ttt180) REVERT: E 407 HIS cc_start: 0.7864 (OUTLIER) cc_final: 0.7249 (p-80) REVERT: E 439 MET cc_start: 0.8842 (mmm) cc_final: 0.8311 (ptt) REVERT: E 476 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8319 (p) REVERT: F 276 MET cc_start: 0.1416 (tpt) cc_final: 0.1172 (tpt) REVERT: F 290 LEU cc_start: 0.8955 (mm) cc_final: 0.8674 (tm) REVERT: F 460 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.6923 (m-80) REVERT: F 552 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7855 (ptt-90) REVERT: A 85 MET cc_start: 0.1475 (mpp) cc_final: 0.1073 (mpp) REVERT: A 246 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8579 (pt) REVERT: A 247 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8767 (mp0) REVERT: A 308 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8224 (mp) REVERT: A 485 MET cc_start: 0.9146 (mtt) cc_final: 0.8923 (mtp) REVERT: A 748 LYS cc_start: 0.9243 (mtpp) cc_final: 0.9036 (mptt) outliers start: 85 outliers final: 48 residues processed: 292 average time/residue: 0.8214 time to fit residues: 284.4320 Evaluate side-chains 281 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 225 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 407 HIS Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 460 TYR Chi-restraints excluded: chain F residue 489 GLU Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain F residue 552 ARG Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 316 optimal weight: 0.9980 chunk 384 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 372 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 394 optimal weight: 50.0000 chunk 108 optimal weight: 5.9990 chunk 380 optimal weight: 5.9990 chunk 365 optimal weight: 5.9990 chunk 366 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** E 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.183265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.106107 restraints weight = 66510.051| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 4.55 r_work: 0.2757 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 37669 Z= 0.181 Angle : 0.654 16.036 51106 Z= 0.319 Chirality : 0.045 0.211 5830 Planarity : 0.005 0.071 6627 Dihedral : 8.007 157.603 5261 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.37 % Allowed : 11.45 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.12), residues: 4662 helix: 1.20 (0.12), residues: 2020 sheet: 0.14 (0.21), residues: 651 loop : -1.87 (0.13), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 212 TYR 0.025 0.001 TYR A 332 PHE 0.026 0.001 PHE B 203 TRP 0.021 0.001 TRP E 292 HIS 0.014 0.001 HIS E 407 Details of bonding type rmsd covalent geometry : bond 0.00439 (37669) covalent geometry : angle 0.65435 (51106) hydrogen bonds : bond 0.04119 ( 1593) hydrogen bonds : angle 4.31951 ( 4620) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 227 time to evaluate : 1.423 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: B 84 VAL cc_start: -0.3433 (OUTLIER) cc_final: -0.3968 (m) REVERT: B 85 MET cc_start: 0.1580 (tpp) cc_final: 0.0743 (ppp) REVERT: B 479 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8275 (mpt180) REVERT: C 323 LYS cc_start: 0.8702 (mmmm) cc_final: 0.8426 (mmtt) REVERT: C 490 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.9021 (mm) REVERT: C 631 GLU cc_start: 0.8331 (mp0) cc_final: 0.7938 (mm-30) REVERT: D 85 MET cc_start: 0.4189 (tpt) cc_final: 0.3809 (pmm) REVERT: D 215 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8886 (pm20) REVERT: D 432 ARG cc_start: 0.8584 (ttt180) cc_final: 0.8278 (ttt180) REVERT: D 479 ARG cc_start: 0.8239 (mmp-170) cc_final: 0.8036 (mmp-170) REVERT: D 545 ARG cc_start: 0.8688 (ttm170) cc_final: 0.8396 (mtm110) REVERT: E 407 HIS cc_start: 0.7871 (OUTLIER) cc_final: 0.7243 (p-80) REVERT: E 439 MET cc_start: 0.8842 (mmm) cc_final: 0.8293 (ptt) REVERT: E 454 HIS cc_start: 0.8456 (m-70) cc_final: 0.8041 (m-70) REVERT: E 476 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8331 (p) REVERT: F 258 MET cc_start: 0.6859 (mpt) cc_final: 0.6309 (mtm) REVERT: F 276 MET cc_start: 0.1360 (tpt) cc_final: 0.1080 (tpt) REVERT: F 290 LEU cc_start: 0.8958 (mm) cc_final: 0.8656 (tm) REVERT: F 460 TYR cc_start: 0.7202 (OUTLIER) cc_final: 0.6555 (m-80) REVERT: A 85 MET cc_start: 0.1632 (mpp) cc_final: 0.1250 (mpp) REVERT: A 246 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8583 (pt) REVERT: A 247 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8728 (mp0) REVERT: A 308 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8196 (mp) REVERT: A 485 MET cc_start: 0.9135 (mtt) cc_final: 0.8905 (mtp) outliers start: 93 outliers final: 53 residues processed: 295 average time/residue: 0.8114 time to fit residues: 285.6714 Evaluate side-chains 282 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 219 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 407 HIS Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 682 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 460 TYR Chi-restraints excluded: chain F residue 489 GLU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 397 optimal weight: 50.0000 chunk 63 optimal weight: 1.9990 chunk 278 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 438 optimal weight: 0.9980 chunk 205 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 175 optimal weight: 9.9990 chunk 243 optimal weight: 30.0000 chunk 371 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 234 GLN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 GLN F 393 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.184282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.107951 restraints weight = 66221.021| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 4.60 r_work: 0.2778 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.119 37669 Z= 0.145 Angle : 0.645 16.598 51106 Z= 0.313 Chirality : 0.044 0.167 5830 Planarity : 0.005 0.069 6627 Dihedral : 7.903 156.639 5261 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.09 % Allowed : 12.04 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.12), residues: 4662 helix: 1.35 (0.12), residues: 2013 sheet: 0.19 (0.20), residues: 653 loop : -1.75 (0.13), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 385 TYR 0.042 0.001 TYR D 135 PHE 0.025 0.001 PHE B 203 TRP 0.022 0.001 TRP E 292 HIS 0.015 0.001 HIS E 407 Details of bonding type rmsd covalent geometry : bond 0.00349 (37669) covalent geometry : angle 0.64473 (51106) hydrogen bonds : bond 0.03737 ( 1593) hydrogen bonds : angle 4.24483 ( 4620) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 236 time to evaluate : 1.472 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: B 84 VAL cc_start: -0.3426 (OUTLIER) cc_final: -0.4037 (m) REVERT: B 85 MET cc_start: 0.1579 (tpp) cc_final: 0.0822 (ppp) REVERT: B 132 PHE cc_start: -0.1586 (OUTLIER) cc_final: -0.1913 (t80) REVERT: B 230 MET cc_start: 0.6576 (mmt) cc_final: 0.6341 (mpm) REVERT: B 295 GLU cc_start: 0.8615 (pt0) cc_final: 0.8401 (pt0) REVERT: B 479 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8238 (mpt180) REVERT: C 230 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.7010 (pmm) REVERT: C 323 LYS cc_start: 0.8656 (mmmm) cc_final: 0.8369 (mmpt) REVERT: C 490 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.8995 (mm) REVERT: C 631 GLU cc_start: 0.8302 (mp0) cc_final: 0.7864 (mm-30) REVERT: D 85 MET cc_start: 0.4186 (tpt) cc_final: 0.3781 (pmm) REVERT: D 215 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8868 (pm20) REVERT: D 432 ARG cc_start: 0.8579 (ttt180) cc_final: 0.8207 (ttt180) REVERT: D 479 ARG cc_start: 0.8203 (mmp-170) cc_final: 0.7990 (mmp-170) REVERT: D 545 ARG cc_start: 0.8659 (ttm170) cc_final: 0.8359 (mtm110) REVERT: E 407 HIS cc_start: 0.7882 (OUTLIER) cc_final: 0.7260 (p-80) REVERT: E 439 MET cc_start: 0.8804 (mmm) cc_final: 0.8258 (ptt) REVERT: E 454 HIS cc_start: 0.8391 (m-70) cc_final: 0.7975 (m-70) REVERT: E 476 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8344 (p) REVERT: F 38 MET cc_start: 0.4504 (pmt) cc_final: 0.3612 (tpt) REVERT: F 50 ARG cc_start: 0.4219 (OUTLIER) cc_final: 0.2894 (mpp-170) REVERT: F 229 GLN cc_start: 0.8991 (pp30) cc_final: 0.8707 (pp30) REVERT: F 258 MET cc_start: 0.6991 (mpt) cc_final: 0.6744 (mtm) REVERT: F 276 MET cc_start: 0.1475 (tpt) cc_final: 0.1171 (tpt) REVERT: F 289 TYR cc_start: 0.7103 (t80) cc_final: 0.6683 (t80) REVERT: F 372 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8718 (ttm) REVERT: F 460 TYR cc_start: 0.7018 (OUTLIER) cc_final: 0.6721 (m-80) REVERT: A 85 MET cc_start: 0.1568 (mpp) cc_final: 0.1190 (mpp) REVERT: A 247 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8777 (mp0) REVERT: A 308 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8198 (mp) REVERT: A 748 LYS cc_start: 0.9074 (mptt) cc_final: 0.8841 (mmmt) outliers start: 82 outliers final: 47 residues processed: 297 average time/residue: 0.8068 time to fit residues: 285.8710 Evaluate side-chains 284 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 224 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 407 HIS Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 682 THR Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 221 GLN Chi-restraints excluded: chain F residue 298 TRP Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 460 TYR Chi-restraints excluded: chain F residue 489 GLU Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain F residue 769 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 101 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 272 optimal weight: 10.0000 chunk 394 optimal weight: 5.9990 chunk 299 optimal weight: 4.9990 chunk 309 optimal weight: 50.0000 chunk 212 optimal weight: 9.9990 chunk 374 optimal weight: 6.9990 chunk 258 optimal weight: 0.0670 chunk 273 optimal weight: 20.0000 chunk 23 optimal weight: 30.0000 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN F 221 GLN ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.183581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.105487 restraints weight = 66670.435| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 4.17 r_work: 0.2813 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 37669 Z= 0.202 Angle : 0.682 17.487 51106 Z= 0.332 Chirality : 0.045 0.179 5830 Planarity : 0.005 0.070 6627 Dihedral : 7.884 155.989 5260 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.14 % Allowed : 11.91 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.81 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.12), residues: 4662 helix: 1.32 (0.12), residues: 2027 sheet: 0.36 (0.21), residues: 641 loop : -1.76 (0.13), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 552 TYR 0.026 0.001 TYR A 332 PHE 0.025 0.001 PHE B 203 TRP 0.025 0.001 TRP E 292 HIS 0.014 0.001 HIS E 407 Details of bonding type rmsd covalent geometry : bond 0.00493 (37669) covalent geometry : angle 0.68205 (51106) hydrogen bonds : bond 0.04221 ( 1593) hydrogen bonds : angle 4.30759 ( 4620) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 229 time to evaluate : 1.620 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: B 132 PHE cc_start: -0.1373 (OUTLIER) cc_final: -0.1729 (t80) REVERT: B 230 MET cc_start: 0.6557 (mmt) cc_final: 0.6318 (mpm) REVERT: B 295 GLU cc_start: 0.8622 (pt0) cc_final: 0.8380 (pt0) REVERT: B 479 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8310 (mpt180) REVERT: C 230 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.7041 (pmm) REVERT: C 318 ASP cc_start: 0.9001 (m-30) cc_final: 0.8700 (m-30) REVERT: C 490 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9066 (mm) REVERT: C 631 GLU cc_start: 0.8363 (mp0) cc_final: 0.7978 (mm-30) REVERT: C 713 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8474 (mtp) REVERT: D 85 MET cc_start: 0.4270 (tpt) cc_final: 0.3745 (pmm) REVERT: D 215 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8841 (pm20) REVERT: D 432 ARG cc_start: 0.8610 (ttt180) cc_final: 0.8242 (ttt180) REVERT: D 545 ARG cc_start: 0.8731 (ttm170) cc_final: 0.8414 (mtm110) REVERT: E 394 ARG cc_start: 0.7177 (tmt170) cc_final: 0.6910 (mmm-85) REVERT: E 407 HIS cc_start: 0.7870 (OUTLIER) cc_final: 0.7253 (p-80) REVERT: E 454 HIS cc_start: 0.8361 (m-70) cc_final: 0.7822 (m-70) REVERT: E 476 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8349 (p) REVERT: F 38 MET cc_start: 0.4401 (pmt) cc_final: 0.3437 (tpt) REVERT: F 276 MET cc_start: 0.1514 (tpt) cc_final: 0.1195 (tpt) REVERT: F 460 TYR cc_start: 0.7077 (OUTLIER) cc_final: 0.6086 (m-80) REVERT: A 85 MET cc_start: 0.1568 (mpp) cc_final: 0.1191 (mpp) REVERT: A 247 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8767 (mp0) REVERT: A 308 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8248 (mp) REVERT: A 439 MET cc_start: 0.9137 (mmp) cc_final: 0.8909 (mmm) REVERT: A 748 LYS cc_start: 0.9088 (mptt) cc_final: 0.8850 (mmmt) outliers start: 84 outliers final: 51 residues processed: 289 average time/residue: 0.8077 time to fit residues: 279.4820 Evaluate side-chains 289 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 227 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 407 HIS Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 682 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 298 TRP Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 460 TYR Chi-restraints excluded: chain F residue 489 GLU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 399 optimal weight: 50.0000 chunk 95 optimal weight: 9.9990 chunk 388 optimal weight: 20.0000 chunk 338 optimal weight: 4.9990 chunk 421 optimal weight: 2.9990 chunk 296 optimal weight: 4.9990 chunk 2 optimal weight: 40.0000 chunk 287 optimal weight: 9.9990 chunk 378 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 245 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 GLN ** F 393 HIS ** 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 = 0.4291 r_free = 0.4291 target = 0.182907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.104742 restraints weight = 66509.429| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 4.66 r_work: 0.2778 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.143 37669 Z= 0.229 Angle : 0.706 17.322 51106 Z= 0.342 Chirality : 0.046 0.207 5830 Planarity : 0.005 0.071 6627 Dihedral : 7.893 156.340 5260 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.83 % Allowed : 12.60 % Favored : 85.57 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.81 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.12), residues: 4662 helix: 1.31 (0.12), residues: 2021 sheet: 0.38 (0.21), residues: 641 loop : -1.73 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 552 TYR 0.023 0.001 TYR D 135 PHE 0.025 0.001 PHE B 203 TRP 0.024 0.001 TRP E 292 HIS 0.014 0.001 HIS E 407 Details of bonding type rmsd covalent geometry : bond 0.00561 (37669) covalent geometry : angle 0.70595 (51106) hydrogen bonds : bond 0.04389 ( 1593) hydrogen bonds : angle 4.36931 ( 4620) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 228 time to evaluate : 1.339 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: B 38 MET cc_start: 0.2556 (mmt) cc_final: 0.2063 (pmm) REVERT: B 132 PHE cc_start: -0.1448 (OUTLIER) cc_final: -0.1790 (t80) REVERT: B 230 MET cc_start: 0.6576 (mmt) cc_final: 0.6361 (mpm) REVERT: B 295 GLU cc_start: 0.8588 (pt0) cc_final: 0.8346 (pt0) REVERT: B 479 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8324 (mpt180) REVERT: C 230 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.7074 (pmm) REVERT: C 490 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.9074 (mm) REVERT: C 631 GLU cc_start: 0.8362 (mp0) cc_final: 0.7962 (mm-30) REVERT: D 85 MET cc_start: 0.4253 (tpt) cc_final: 0.3747 (pmm) REVERT: D 432 ARG cc_start: 0.8605 (ttt180) cc_final: 0.8337 (ttt180) REVERT: D 479 ARG cc_start: 0.8394 (mmm160) cc_final: 0.7972 (mmp-170) REVERT: D 545 ARG cc_start: 0.8709 (ttm170) cc_final: 0.8405 (mtm110) REVERT: D 546 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7788 (mp0) REVERT: E 394 ARG cc_start: 0.7177 (tmt170) cc_final: 0.6929 (mmm-85) REVERT: E 439 MET cc_start: 0.8606 (mmm) cc_final: 0.8111 (mtm) REVERT: E 454 HIS cc_start: 0.8372 (m-70) cc_final: 0.8136 (m170) REVERT: E 476 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8313 (p) REVERT: F 50 ARG cc_start: 0.4250 (OUTLIER) cc_final: 0.2952 (mpp-170) REVERT: F 276 MET cc_start: 0.1556 (tpt) cc_final: 0.1234 (tpt) REVERT: F 289 TYR cc_start: 0.7311 (t80) cc_final: 0.6473 (t80) REVERT: F 460 TYR cc_start: 0.6622 (OUTLIER) cc_final: 0.5963 (m-80) REVERT: F 461 ASP cc_start: 0.8797 (t0) cc_final: 0.8535 (t0) REVERT: A 85 MET cc_start: 0.1468 (mpp) cc_final: 0.1118 (mpp) REVERT: A 247 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8769 (mp0) REVERT: A 308 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8227 (mp) REVERT: A 748 LYS cc_start: 0.9071 (mptt) cc_final: 0.8838 (mmmt) outliers start: 72 outliers final: 51 residues processed: 282 average time/residue: 0.7902 time to fit residues: 264.7664 Evaluate side-chains 285 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 225 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 594 VAL Chi-restraints excluded: chain E residue 682 THR Chi-restraints excluded: chain F residue 50 ARG Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 221 GLN Chi-restraints excluded: chain F residue 298 TRP Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 460 TYR Chi-restraints excluded: chain F residue 489 GLU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 522 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 97 optimal weight: 20.0000 chunk 199 optimal weight: 3.9990 chunk 221 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 340 optimal weight: 10.0000 chunk 341 optimal weight: 2.9990 chunk 299 optimal weight: 0.9980 chunk 277 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 454 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 GLN ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.183182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105374 restraints weight = 66215.115| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 4.33 r_work: 0.2765 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.283 37669 Z= 0.239 Angle : 0.777 59.199 51106 Z= 0.398 Chirality : 0.047 0.789 5830 Planarity : 0.005 0.071 6627 Dihedral : 7.893 156.372 5260 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.70 % Allowed : 12.72 % Favored : 85.57 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.81 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.12), residues: 4662 helix: 1.31 (0.12), residues: 2021 sheet: 0.38 (0.21), residues: 641 loop : -1.73 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.000 ARG F 395 TYR 0.098 0.002 TYR F 289 PHE 0.025 0.001 PHE B 203 TRP 0.020 0.001 TRP E 292 HIS 0.014 0.001 HIS E 407 Details of bonding type rmsd covalent geometry : bond 0.00574 (37669) covalent geometry : angle 0.77663 (51106) hydrogen bonds : bond 0.04319 ( 1593) hydrogen bonds : angle 4.37061 ( 4620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25170.97 seconds wall clock time: 425 minutes 45.79 seconds (25545.79 seconds total)