Starting phenix.real_space_refine on Sat Feb 7 21:11:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fie_31590/02_2026/7fie_31590.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fie_31590/02_2026/7fie_31590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fie_31590/02_2026/7fie_31590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fie_31590/02_2026/7fie_31590.map" model { file = "/net/cci-nas-00/data/ceres_data/7fie_31590/02_2026/7fie_31590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fie_31590/02_2026/7fie_31590.cif" } resolution = 2.36 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 16 5.49 5 S 136 5.16 5 C 23328 2.51 5 N 6490 2.21 5 O 7027 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36997 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': 2, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 730} Chain: "C" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 730} 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': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} 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': 2, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 730} Chain: "S" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 111 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 21} Unresolved non-hydrogen planarities: 21 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 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: 9.78, per 1000 atoms: 0.26 Number of scatterers: 36997 At special positions: 0 Unit cell: (182.04, 200.08, 218.94, 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 136 16.00 P 16 15.00 O 7027 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: 3.18 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 41 sheets defined 46.6% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'B' and resid 30 through 36 Processing helix chain 'B' and resid 58 through 62 removed outlier: 3.639A pdb=" N ASP B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 62 " --> pdb=" O PRO B 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 58 through 62' Processing helix chain 'B' and resid 117 through 136 removed outlier: 3.910A pdb=" N LYS B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 139 No H-bonds generated for 'chain 'B' and resid 137 through 139' Processing helix chain 'B' and resid 157 through 169 removed outlier: 4.341A pdb=" N HIS B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 182 removed outlier: 4.161A pdb=" N GLN B 177 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 237 removed outlier: 3.712A pdb=" N ARG B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 256 removed outlier: 3.720A pdb=" N GLU B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 256 " --> pdb=" O LYS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.866A pdb=" N THR B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 296 " --> pdb=" O TRP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 319 removed outlier: 3.834A pdb=" N ASP B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 338 removed outlier: 3.541A pdb=" N LYS B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 372 removed outlier: 4.247A pdb=" N ARG B 366 " --> pdb=" O THR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.562A pdb=" N GLU B 389 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 412 Processing helix chain 'B' and resid 434 through 438 removed outlier: 3.732A pdb=" N SER B 437 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 450 Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.743A pdb=" N ASP B 483 " --> pdb=" O ARG B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 505 through 514 removed outlier: 3.843A pdb=" N LYS B 509 " --> pdb=" O TYR B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.777A pdb=" N THR B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 561 removed outlier: 3.538A pdb=" N LEU B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 572 No H-bonds generated for 'chain 'B' and resid 570 through 572' Processing helix chain 'B' and resid 573 through 579 removed outlier: 3.981A pdb=" N TYR B 577 " --> pdb=" O ASP B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 646 removed outlier: 3.621A pdb=" N ALA B 646 " --> pdb=" O THR B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 717 through 729 Processing helix chain 'B' and resid 738 through 746 removed outlier: 4.548A pdb=" N ALA B 741 " --> pdb=" O ASP B 738 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU B 744 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 745 " --> pdb=" O GLN B 742 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 746 " --> pdb=" O LEU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.524A pdb=" N GLU B 752 " --> pdb=" O LYS B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 770 removed outlier: 3.876A pdb=" N VAL B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 39 Processing helix chain 'C' and resid 117 through 136 removed outlier: 3.527A pdb=" N VAL C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 169 removed outlier: 3.534A pdb=" N ALA C 166 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR C 167 " --> pdb=" O ASP C 163 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA C 169 " --> pdb=" O ILE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 179 Processing helix chain 'C' and resid 186 through 236 removed outlier: 3.509A pdb=" N GLU C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 256 removed outlier: 3.893A pdb=" N GLU C 254 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 274 removed outlier: 3.995A pdb=" N LYS C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 296 removed outlier: 4.069A pdb=" N ALA C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 296 " --> pdb=" O TRP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 315 removed outlier: 3.758A pdb=" N GLN C 313 " --> pdb=" O ASN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 322 through 339 Processing helix chain 'C' and resid 362 through 372 removed outlier: 4.390A pdb=" N ARG C 366 " --> pdb=" O THR C 362 " (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 423 through 427 removed outlier: 3.918A pdb=" N MET C 427 " --> pdb=" O ILE C 424 " (cutoff:3.500A) 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 513 removed outlier: 3.644A pdb=" N LYS C 509 " --> pdb=" O TYR C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.892A pdb=" N THR C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 561 removed outlier: 3.575A pdb=" N LEU C 559 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 560 " --> pdb=" O LYS C 556 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY C 561 " --> pdb=" O PHE C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 579 removed outlier: 3.844A pdb=" N TYR C 577 " --> pdb=" O ASP C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 646 removed outlier: 3.703A pdb=" N ALA C 646 " --> pdb=" O THR C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 652 removed outlier: 3.921A pdb=" N TYR C 651 " --> pdb=" O HIS C 647 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY C 652 " --> pdb=" O THR C 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 647 through 652' Processing helix chain 'C' and resid 679 through 693 Processing helix chain 'C' and resid 717 through 728 removed outlier: 3.662A pdb=" N LYS C 721 " --> pdb=" O GLY C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 746 removed outlier: 4.649A pdb=" N ALA C 741 " --> pdb=" O ASP C 738 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN C 742 " --> pdb=" O ASN C 739 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU C 744 " --> pdb=" O ALA C 741 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 746 " --> pdb=" O LEU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 754 removed outlier: 3.603A pdb=" N GLU C 752 " --> pdb=" O LYS C 748 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY C 753 " --> pdb=" O GLU C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 770 removed outlier: 3.957A pdb=" N VAL C 765 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 770 " --> pdb=" O LEU C 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 36 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 58 through 62 removed outlier: 3.655A pdb=" N ASP D 61 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU D 62 " --> pdb=" O PRO D 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 58 through 62' Processing helix chain 'D' and resid 117 through 138 removed outlier: 3.620A pdb=" N VAL D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 169 removed outlier: 4.064A pdb=" N LEU D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA D 169 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 182 removed outlier: 3.545A pdb=" N LYS D 176 " --> pdb=" O THR D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 235 removed outlier: 3.759A pdb=" N LEU D 189 " --> pdb=" O LEU D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 256 removed outlier: 3.529A pdb=" N GLU D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 276 removed outlier: 3.730A pdb=" N MET D 276 " --> pdb=" O ARG D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.770A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRP D 292 " --> pdb=" O THR D 288 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.697A pdb=" N ASP D 316 " --> pdb=" O ARG D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 339 removed outlier: 3.550A pdb=" N LYS D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 372 removed outlier: 3.870A pdb=" N GLY D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG D 366 " --> pdb=" O THR D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 390 removed outlier: 3.932A 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 Processing helix chain 'D' and resid 434 through 443 removed outlier: 3.781A pdb=" N ALA D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU D 441 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 450 removed outlier: 3.501A pdb=" N THR D 450 " --> pdb=" O GLN D 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 447 through 450' Processing helix chain 'D' and resid 478 through 484 removed outlier: 3.800A pdb=" N ARG D 484 " --> pdb=" O PRO D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 505 through 515 removed outlier: 3.539A pdb=" N LYS D 509 " --> pdb=" O TYR D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.837A 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 570 through 572 No H-bonds generated for 'chain 'D' and resid 570 through 572' Processing helix chain 'D' and resid 573 through 579 removed outlier: 3.639A pdb=" N TYR D 577 " --> pdb=" O ASP D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 647 removed outlier: 3.571A pdb=" N ALA D 646 " --> pdb=" O THR D 642 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 692 removed outlier: 3.615A pdb=" N SER D 692 " --> pdb=" O ALA D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 728 removed outlier: 3.587A pdb=" N LYS D 721 " --> pdb=" O GLY D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 746 removed outlier: 4.759A pdb=" N ALA D 741 " --> pdb=" O ASP D 738 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU D 744 " --> pdb=" O ALA D 741 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU D 745 " --> pdb=" O GLN D 742 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU D 746 " --> pdb=" O LEU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 770 removed outlier: 3.734A pdb=" N VAL D 765 " --> pdb=" O ASP D 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 39 removed outlier: 4.038A pdb=" N ALA E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 137 removed outlier: 4.062A pdb=" N ALA E 137 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 152 removed outlier: 3.651A pdb=" N GLU E 150 " --> pdb=" O TYR E 147 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA E 151 " --> pdb=" O GLN E 148 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL E 152 " --> pdb=" O LEU E 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 147 through 152' Processing helix chain 'E' and resid 157 through 169 removed outlier: 3.520A pdb=" N LEU E 161 " --> pdb=" O ASP E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 181 Processing helix chain 'E' and resid 184 through 234 removed outlier: 3.827A pdb=" N ARG E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 237 No H-bonds generated for 'chain 'E' and resid 235 through 237' Processing helix chain 'E' and resid 244 through 256 removed outlier: 3.764A pdb=" N VAL E 256 " --> pdb=" O LYS E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 275 removed outlier: 3.875A pdb=" N ARG E 275 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 295 removed outlier: 3.630A pdb=" N THR E 284 " --> pdb=" O SER E 280 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 317 Processing helix chain 'E' and resid 322 through 339 removed outlier: 3.627A pdb=" N LYS E 326 " --> pdb=" O LEU E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 373 removed outlier: 3.563A pdb=" N LEU E 364 " --> pdb=" O GLY E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 412 removed outlier: 3.537A pdb=" N GLN E 411 " --> pdb=" O HIS E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 427 removed outlier: 3.730A pdb=" N LYS E 426 " --> pdb=" O GLU E 423 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET E 427 " --> pdb=" O ILE E 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 423 through 427' Processing helix chain 'E' and resid 437 through 442 removed outlier: 3.634A pdb=" N LEU E 440 " --> pdb=" O SER E 437 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU E 441 " --> pdb=" O ALA E 438 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL E 442 " --> pdb=" O MET E 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 437 through 442' Processing helix chain 'E' and resid 478 through 483 removed outlier: 3.561A pdb=" N ASP E 483 " --> pdb=" O ARG E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 505 Processing helix chain 'E' and resid 505 through 513 removed outlier: 3.725A pdb=" N LYS E 509 " --> pdb=" O TYR E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.820A pdb=" N THR E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 561 removed outlier: 3.601A pdb=" N LEU E 559 " --> pdb=" O ALA E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 579 removed outlier: 3.787A pdb=" N TYR E 577 " --> pdb=" O ASP E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 647 Processing helix chain 'E' and resid 647 through 652 removed outlier: 4.174A pdb=" N TYR E 651 " --> pdb=" O HIS E 647 " (cutoff:3.500A) removed outlier: 3.646A 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 Processing helix chain 'E' and resid 717 through 728 removed outlier: 3.657A pdb=" N LYS E 721 " --> pdb=" O GLY E 717 " (cutoff:3.500A) Processing helix chain 'E' and resid 738 through 746 removed outlier: 4.866A pdb=" N ALA E 741 " --> pdb=" O ASP E 738 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU E 746 " --> pdb=" O LEU E 743 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 754 removed outlier: 3.621A pdb=" N GLY E 753 " --> pdb=" O GLU E 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 770 removed outlier: 3.999A pdb=" N VAL E 765 " --> pdb=" O ASP E 761 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU E 770 " --> pdb=" O LEU E 766 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 39 removed outlier: 3.758A pdb=" N MET F 38 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 137 removed outlier: 3.916A pdb=" N VAL F 121 " --> pdb=" O ASP F 117 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA F 137 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 150 removed outlier: 4.363A pdb=" N LEU F 149 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU F 150 " --> pdb=" O TYR F 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 146 through 150' Processing helix chain 'F' and resid 157 through 169 Processing helix chain 'F' and resid 172 through 181 removed outlier: 3.728A pdb=" N LYS F 176 " --> pdb=" O THR F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 235 Processing helix chain 'F' and resid 248 through 253 removed outlier: 3.627A pdb=" N ILE F 253 " --> pdb=" O LEU F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 271 Processing helix chain 'F' and resid 280 through 295 removed outlier: 3.715A pdb=" N THR F 284 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU F 295 " --> pdb=" O ASP F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 316 removed outlier: 3.594A pdb=" N ASP F 316 " --> pdb=" O ARG F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 339 removed outlier: 4.094A pdb=" N TYR F 332 " --> pdb=" O ARG F 328 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU F 338 " --> pdb=" O ALA F 334 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR F 339 " --> pdb=" O VAL F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 371 Processing helix chain 'F' and resid 386 through 390 removed outlier: 4.049A pdb=" N GLU F 389 " --> pdb=" O ASP F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 410 Processing helix chain 'F' and resid 434 through 444 removed outlier: 4.021A pdb=" N ALA F 438 " --> pdb=" O ASP F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 484 removed outlier: 3.877A pdb=" N ASP F 483 " --> pdb=" O ARG F 479 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG F 484 " --> pdb=" O PRO F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 505 Processing helix chain 'F' and resid 505 through 513 removed outlier: 3.676A pdb=" N LYS F 509 " --> pdb=" O TYR F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.550A pdb=" N ILE F 527 " --> pdb=" O THR F 523 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR F 535 " --> pdb=" O ILE F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 561 Processing helix chain 'F' and resid 570 through 572 No H-bonds generated for 'chain 'F' and resid 570 through 572' Processing helix chain 'F' and resid 573 through 579 removed outlier: 3.690A pdb=" N TYR F 577 " --> pdb=" O ASP F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 646 removed outlier: 3.536A pdb=" N ALA F 646 " --> pdb=" O THR F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 679 through 693 Processing helix chain 'F' and resid 717 through 727 removed outlier: 3.642A pdb=" N LYS F 721 " --> pdb=" O GLY F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 746 removed outlier: 4.801A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU F 743 " --> pdb=" O GLU F 740 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU F 744 " --> pdb=" O ALA F 741 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU F 745 " --> pdb=" O GLN F 742 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU F 746 " --> pdb=" O LEU F 743 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 754 removed outlier: 4.251A pdb=" N GLY F 753 " --> pdb=" O GLU F 749 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU F 754 " --> pdb=" O VAL F 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 749 through 754' Processing helix chain 'F' and resid 761 through 770 removed outlier: 3.740A pdb=" N VAL F 765 " --> pdb=" O ASP F 761 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU F 770 " --> pdb=" O LEU F 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 39 removed outlier: 4.235A pdb=" N VAL A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 138 Processing helix chain 'A' and resid 146 through 151 removed outlier: 3.803A pdb=" N GLU A 150 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 168 removed outlier: 3.879A pdb=" N TYR A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 186 through 235 Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 248 through 257 removed outlier: 4.176A pdb=" N GLU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 276 removed outlier: 5.648A pdb=" N ARG A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 295 removed outlier: 3.826A pdb=" N ALA A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.692A pdb=" N THR A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 339 Processing helix chain 'A' and resid 360 through 372 removed outlier: 3.562A pdb=" N LEU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG A 366 " --> pdb=" O THR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.926A pdb=" N GLU A 389 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 412 Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.519A pdb=" N LYS A 426 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.992A 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: 4.144A pdb=" N ALA A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 removed outlier: 3.725A pdb=" N THR A 450 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 451 " --> pdb=" O ASN A 448 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 447 through 451' Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 513 removed outlier: 3.662A pdb=" N LYS A 509 " --> pdb=" O TYR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.758A pdb=" N THR A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 560 removed outlier: 3.711A pdb=" N LEU A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.853A 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 679 through 693 Processing helix chain 'A' and resid 717 through 728 removed outlier: 3.561A pdb=" N ALA A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 746 removed outlier: 3.865A pdb=" N GLU A 745 " --> pdb=" O GLN A 742 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 746 " --> pdb=" O LEU A 743 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 742 through 746' Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.667A pdb=" N GLY A 753 " --> pdb=" O GLU A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 770 removed outlier: 3.935A pdb=" N VAL A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'B' and resid 24 through 25 removed outlier: 4.275A pdb=" N VAL B 25 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 82 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL B 84 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA B 74 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL B 86 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS B 72 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ALA B 88 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 70 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA B 90 " --> pdb=" O GLN B 68 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY B 66 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 375 through 379 removed outlier: 7.624A pdb=" N ILE B 468 " --> pdb=" O PRO B 417 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE B 419 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N THR B 470 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU B 421 " --> pdb=" O THR B 470 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU B 351 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ALA B 471 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU B 353 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE B 350 " --> pdb=" O GLU B 486 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE B 488 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL B 352 " --> pdb=" O ILE B 488 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 451 through 452 Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522 Processing sheet with id=AA6, first strand: chain 'B' and resid 622 through 626 removed outlier: 5.893A pdb=" N LYS B 622 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL B 665 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER B 624 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N MET B 702 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN B 598 " --> pdb=" O MET B 702 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 705 through 706 Processing sheet with id=AA8, first strand: chain 'C' and resid 8 through 9 removed outlier: 3.654A pdb=" N VAL C 47 " --> pdb=" O ILE C 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 23 through 24 removed outlier: 3.619A pdb=" N VAL C 23 " --> pdb=" O LEU C 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 376 through 380 removed outlier: 6.197A pdb=" N ILE C 419 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N THR C 470 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU C 421 " --> pdb=" O THR C 470 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU C 351 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ALA C 471 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N LEU C 353 " --> pdb=" O ALA C 471 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE C 350 " --> pdb=" O GLU C 486 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ILE C 488 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL C 352 " --> pdb=" O ILE C 488 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 520 through 522 removed outlier: 6.940A pdb=" N GLU C 521 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 596 through 602 removed outlier: 6.114A pdb=" N LYS C 622 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL C 665 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.861A pdb=" N ALA C 701 " --> pdb=" O VAL C 734 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 733 " --> pdb=" O LYS C 757 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL C 759 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU C 735 " --> pdb=" O VAL C 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 705 through 706 Processing sheet with id=AB6, first strand: chain 'D' and resid 20 through 22 removed outlier: 3.880A pdb=" N THR D 21 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL D 86 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL D 84 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA D 74 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VAL D 86 " --> pdb=" O LYS D 72 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LYS D 72 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ALA D 88 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL D 70 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA D 90 " --> pdb=" O GLN D 68 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 376 through 380 removed outlier: 3.555A pdb=" N THR D 470 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 451 through 452 Processing sheet with id=AB9, first strand: chain 'D' and resid 520 through 522 removed outlier: 6.825A pdb=" N GLU D 521 " --> pdb=" O ILE D 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 596 through 603 removed outlier: 6.367A pdb=" N SER D 624 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 701 through 702 Processing sheet with id=AC3, first strand: chain 'D' and resid 705 through 706 removed outlier: 3.580A pdb=" N GLU D 705 " --> pdb=" O MET D 713 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 19 through 24 removed outlier: 3.701A pdb=" N THR E 19 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA E 88 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU E 82 " --> pdb=" O ARG E 76 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG E 76 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL E 84 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA E 74 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL E 86 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS E 72 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ALA E 88 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL E 70 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA E 90 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY E 66 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA E 69 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE E 44 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 97 through 98 Processing sheet with id=AC6, first strand: chain 'E' and resid 375 through 380 removed outlier: 6.232A pdb=" N LYS E 375 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LEU E 420 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N HIS E 377 " --> pdb=" O LEU E 420 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASP E 422 " --> pdb=" O HIS E 377 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE E 379 " --> pdb=" O ASP E 422 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU E 351 " --> pdb=" O PHE E 467 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR E 469 " --> pdb=" O LEU E 351 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE E 350 " --> pdb=" O GLU E 486 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE E 488 " --> pdb=" O ILE E 350 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL E 352 " --> pdb=" O ILE E 488 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 451 through 452 Processing sheet with id=AC8, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.499A 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 593 through 594 Processing sheet with id=AD1, first strand: chain 'E' and resid 596 through 603 removed outlier: 6.024A pdb=" N LYS E 622 " --> pdb=" O LEU E 663 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL E 665 " --> pdb=" O LYS E 622 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER E 624 " --> pdb=" O VAL E 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 701 through 702 removed outlier: 6.537A pdb=" N ILE E 733 " --> pdb=" O LYS E 757 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL E 759 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU E 735 " --> pdb=" O VAL E 759 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 705 through 706 Processing sheet with id=AD4, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.916A pdb=" N LEU F 5 " --> pdb=" O ALA F 105 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA F 105 " --> pdb=" O LEU F 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'F' and resid 20 through 25 removed outlier: 3.566A pdb=" N VAL F 84 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL F 25 " --> pdb=" O LEU F 82 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N GLN F 83 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA F 74 " --> pdb=" O GLN F 83 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N MET F 85 " --> pdb=" O LYS F 72 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLN F 68 " --> pdb=" O ARG F 89 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ARG F 91 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N GLY F 66 " --> pdb=" O ARG F 91 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA F 69 " --> pdb=" O ILE F 44 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE F 44 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 376 through 378 removed outlier: 7.461A pdb=" N HIS F 377 " --> pdb=" O LEU F 420 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N ASP F 422 " --> pdb=" O HIS F 377 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILE F 419 " --> pdb=" O ILE F 468 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N THR F 470 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU F 421 " --> pdb=" O THR F 470 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU F 351 " --> pdb=" O THR F 469 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ALA F 471 " --> pdb=" O LEU F 351 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU F 353 " --> pdb=" O ALA F 471 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL F 352 " --> pdb=" O GLU F 486 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 520 through 522 removed outlier: 6.617A pdb=" N GLU F 521 " --> pdb=" O ILE F 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'F' and resid 596 through 603 removed outlier: 5.926A pdb=" N LYS F 622 " --> pdb=" O LEU F 663 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL F 665 " --> pdb=" O LYS F 622 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER F 624 " --> pdb=" O VAL F 665 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 701 through 702 removed outlier: 6.890A pdb=" N ALA F 701 " --> pdb=" O VAL F 734 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE F 733 " --> pdb=" O LYS F 757 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL F 759 " --> pdb=" O ILE F 733 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU F 735 " --> pdb=" O VAL F 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'F' and resid 705 through 706 Processing sheet with id=AE2, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.523A pdb=" N THR A 470 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU A 351 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ALA A 471 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEU A 353 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL A 352 " --> pdb=" O ILE A 488 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.975A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'A' and resid 623 through 626 removed outlier: 6.542A pdb=" N SER A 624 " --> pdb=" O VAL A 665 " (cutoff:3.500A) removed outlier: 10.004A pdb=" N MET A 702 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLN A 598 " --> pdb=" O MET A 702 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE A 733 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL A 759 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU A 735 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 705 through 706 1500 hydrogen bonds defined for protein. 4353 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: 8.33 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.29: 6398 1.29 - 1.45: 9573 1.45 - 1.62: 21435 1.62 - 1.78: 44 1.78 - 1.95: 224 Bond restraints: 37674 Sorted by residual: bond pdb=" C ASP D 675 " pdb=" O ASP D 675 " ideal model delta sigma weight residual 1.234 1.122 0.112 1.20e-02 6.94e+03 8.65e+01 bond pdb=" C ASP E 675 " pdb=" O ASP E 675 " ideal model delta sigma weight residual 1.233 1.127 0.106 1.17e-02 7.31e+03 8.23e+01 bond pdb=" C ASP F 675 " pdb=" O ASP F 675 " ideal model delta sigma weight residual 1.233 1.128 0.105 1.17e-02 7.31e+03 8.05e+01 bond pdb=" C ASP A 675 " pdb=" O ASP A 675 " ideal model delta sigma weight residual 1.233 1.129 0.105 1.17e-02 7.31e+03 7.98e+01 bond pdb=" C ASP C 675 " pdb=" O ASP C 675 " ideal model delta sigma weight residual 1.234 1.127 0.107 1.20e-02 6.94e+03 7.94e+01 ... (remaining 37669 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 50286 3.45 - 6.89: 716 6.89 - 10.34: 86 10.34 - 13.78: 20 13.78 - 17.23: 7 Bond angle restraints: 51115 Sorted by residual: angle pdb=" O ASP D 675 " pdb=" C ASP D 675 " pdb=" N GLY D 676 " ideal model delta sigma weight residual 123.42 106.19 17.23 1.07e+00 8.73e-01 2.59e+02 angle pdb=" O ASP A 675 " pdb=" C ASP A 675 " pdb=" N GLY A 676 " ideal model delta sigma weight residual 123.26 107.51 15.75 1.05e+00 9.07e-01 2.25e+02 angle pdb=" O ASP E 675 " pdb=" C ASP E 675 " pdb=" N GLY E 676 " ideal model delta sigma weight residual 123.26 107.67 15.59 1.05e+00 9.07e-01 2.21e+02 angle pdb=" O ASP F 675 " pdb=" C ASP F 675 " pdb=" N GLY F 676 " ideal model delta sigma weight residual 123.26 107.75 15.51 1.05e+00 9.07e-01 2.18e+02 angle pdb=" O ASP C 675 " pdb=" C ASP C 675 " pdb=" N GLY C 676 " ideal model delta sigma weight residual 123.42 107.67 15.75 1.07e+00 8.73e-01 2.17e+02 ... (remaining 51110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 23033 35.62 - 71.25: 208 71.25 - 106.87: 24 106.87 - 142.49: 5 142.49 - 178.11: 3 Dihedral angle restraints: 23273 sinusoidal: 9714 harmonic: 13559 Sorted by residual: dihedral pdb=" CA GLN B 278 " pdb=" C GLN B 278 " pdb=" N GLY B 279 " pdb=" CA GLY B 279 " ideal model delta harmonic sigma weight residual -180.00 -132.21 -47.79 0 5.00e+00 4.00e-02 9.14e+01 dihedral pdb=" CA ASN F 416 " pdb=" C ASN F 416 " pdb=" N PRO F 417 " pdb=" CA PRO F 417 " ideal model delta harmonic sigma weight residual -180.00 -145.26 -34.74 0 5.00e+00 4.00e-02 4.83e+01 dihedral pdb=" C2' ADP F 901 " pdb=" C1' ADP F 901 " pdb=" N9 ADP F 901 " pdb=" C4 ADP F 901 " ideal model delta sinusoidal sigma weight residual 91.55 -86.57 178.11 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 23270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 5212 0.097 - 0.193: 572 0.193 - 0.290: 42 0.290 - 0.387: 5 0.387 - 0.484: 1 Chirality restraints: 5832 Sorted by residual: chirality pdb=" CA GLU D 423 " pdb=" N GLU D 423 " pdb=" C GLU D 423 " pdb=" CB GLU D 423 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" CA LEU B 237 " pdb=" N LEU B 237 " pdb=" C LEU B 237 " pdb=" CB LEU B 237 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" C3' ADP E 901 " pdb=" C2' ADP E 901 " pdb=" C4' ADP E 901 " pdb=" O3' ADP E 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.83 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 5829 not shown) Planarity restraints: 6628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 675 " -0.089 2.00e-02 2.50e+03 1.76e-01 3.10e+02 pdb=" C ASP C 675 " 0.303 2.00e-02 2.50e+03 pdb=" O ASP C 675 " -0.136 2.00e-02 2.50e+03 pdb=" N GLY C 676 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 675 " -0.089 2.00e-02 2.50e+03 1.76e-01 3.10e+02 pdb=" C ASP E 675 " 0.303 2.00e-02 2.50e+03 pdb=" O ASP E 675 " -0.136 2.00e-02 2.50e+03 pdb=" N GLY E 676 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 675 " 0.089 2.00e-02 2.50e+03 1.75e-01 3.08e+02 pdb=" C ASP B 675 " -0.302 2.00e-02 2.50e+03 pdb=" O ASP B 675 " 0.136 2.00e-02 2.50e+03 pdb=" N GLY B 676 " 0.077 2.00e-02 2.50e+03 ... (remaining 6625 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6862 2.77 - 3.31: 32121 3.31 - 3.84: 58594 3.84 - 4.37: 66854 4.37 - 4.90: 116373 Nonbonded interactions: 280804 Sorted by model distance: nonbonded pdb=" N GLY B 279 " pdb=" N SER B 280 " model vdw 2.243 2.560 nonbonded pdb=" O VAL B 359 " pdb=" O2B AGS B 901 " model vdw 2.266 3.040 nonbonded pdb=" O LYS A 268 " pdb=" NH1 ARG A 272 " model vdw 2.270 3.120 nonbonded pdb=" N ASP C 245 " pdb=" OD1 ASP C 245 " model vdw 2.276 3.120 nonbonded pdb=" OG1 THR A 603 " pdb=" O GLY A 606 " model vdw 2.281 3.040 ... (remaining 280799 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.890 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 35.610 Find NCS groups from input model: 1.130 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:8.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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 : 0.008 0.113 37674 Z= 0.404 Angle : 1.107 17.230 51115 Z= 0.659 Chirality : 0.062 0.484 5832 Planarity : 0.009 0.176 6628 Dihedral : 11.619 178.114 14541 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.18 % Favored : 95.67 % Rotamer: Outliers : 0.89 % Allowed : 4.22 % Favored : 94.89 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.34 % Twisted Proline : 0.36 % 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: -3.44 (0.10), residues: 4662 helix: -2.33 (0.09), residues: 1909 sheet: -0.51 (0.21), residues: 541 loop : -2.68 (0.10), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG C 198 TYR 0.038 0.003 TYR F 225 PHE 0.034 0.003 PHE C 132 TRP 0.028 0.003 TRP A 171 HIS 0.013 0.002 HIS C 454 Details of bonding type rmsd covalent geometry : bond 0.00783 (37674) covalent geometry : angle 1.10687 (51115) hydrogen bonds : bond 0.16999 ( 1500) hydrogen bonds : angle 7.08938 ( 4353) *********************** 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 456 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 421 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 398 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8139 (mp) REVERT: C 331 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8087 (pt0) REVERT: A 62 LEU cc_start: 0.1391 (OUTLIER) cc_final: 0.0836 (mp) outliers start: 35 outliers final: 5 residues processed: 452 average time/residue: 0.9149 time to fit residues: 479.4740 Evaluate side-chains 252 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 244 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 678 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 8.9990 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 50.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 ASN B 168 HIS ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 HIS C 49 GLN C 177 GLN C 377 HIS ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 HIS D 168 HIS D 229 GLN D 504 GLN D 739 ASN E 83 GLN E 138 ASN E 220 ASN E 340 GLN E 472 ASN E 510 GLN E 647 HIS F 229 GLN F 472 ASN F 598 GLN ** F 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A 628 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.179392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.105617 restraints weight = 66250.002| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.68 r_work: 0.2947 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 37674 Z= 0.171 Angle : 0.662 15.661 51115 Z= 0.335 Chirality : 0.046 0.177 5832 Planarity : 0.005 0.056 6628 Dihedral : 8.424 176.828 5278 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.22 % Rotamer: Outliers : 1.98 % Allowed : 9.16 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.34 % Twisted Proline : 0.00 % 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: -1.76 (0.11), residues: 4662 helix: -0.39 (0.11), residues: 1948 sheet: -0.14 (0.21), residues: 563 loop : -2.21 (0.11), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 328 TYR 0.027 0.001 TYR F 224 PHE 0.024 0.001 PHE C 110 TRP 0.018 0.002 TRP E 602 HIS 0.008 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00399 (37674) covalent geometry : angle 0.66176 (51115) hydrogen bonds : bond 0.04784 ( 1500) hydrogen bonds : angle 5.02199 ( 4353) *********************** 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 332 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 254 time to evaluate : 1.530 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 230 MET cc_start: 0.7048 (mtm) cc_final: 0.6737 (mpp) REVERT: B 398 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8183 (mp) REVERT: B 416 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8524 (p0) REVERT: C 82 LEU cc_start: 0.0452 (OUTLIER) cc_final: 0.0215 (mt) REVERT: D 587 LYS cc_start: 0.9001 (pttt) cc_final: 0.8791 (pttm) REVERT: D 699 ASP cc_start: 0.8840 (t70) cc_final: 0.8445 (t0) REVERT: E 149 LEU cc_start: 0.3566 (OUTLIER) cc_final: 0.3142 (pt) REVERT: E 393 HIS cc_start: 0.6862 (OUTLIER) cc_final: 0.6229 (t-170) REVERT: E 424 ILE cc_start: 0.8750 (tt) cc_final: 0.8519 (pp) REVERT: E 441 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7635 (mm-30) REVERT: E 442 VAL cc_start: 0.8914 (m) cc_final: 0.8711 (p) REVERT: E 602 TRP cc_start: 0.8902 (t60) cc_final: 0.8661 (t60) REVERT: F 324 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7826 (t0) REVERT: F 328 ARG cc_start: 0.8716 (ttm110) cc_final: 0.8401 (ttm-80) REVERT: F 479 ARG cc_start: 0.8395 (mmm160) cc_final: 0.8163 (mmm160) REVERT: F 483 ASP cc_start: 0.8727 (m-30) cc_final: 0.8357 (m-30) REVERT: F 541 ARG cc_start: 0.8059 (mmm-85) cc_final: 0.7642 (mtt-85) REVERT: A 47 VAL cc_start: -0.1048 (OUTLIER) cc_final: -0.1504 (t) REVERT: A 62 LEU cc_start: 0.1981 (OUTLIER) cc_final: 0.1010 (mp) REVERT: A 191 LYS cc_start: 0.5029 (OUTLIER) cc_final: 0.4441 (mppt) REVERT: A 274 GLU cc_start: 0.9007 (tp30) cc_final: 0.8803 (mm-30) REVERT: A 398 ILE cc_start: 0.9018 (tt) cc_final: 0.8003 (mm) outliers start: 78 outliers final: 19 residues processed: 313 average time/residue: 0.8782 time to fit residues: 325.3330 Evaluate side-chains 252 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 674 LYS Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 385 ARG Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 452 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 207 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 356 optimal weight: 8.9990 chunk 258 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 316 optimal weight: 50.0000 chunk 128 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 237 optimal weight: 30.0000 chunk 239 optimal weight: 20.0000 chunk 279 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 GLN E 229 GLN ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 HIS F 472 ASN A 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.177795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102964 restraints weight = 65844.598| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.63 r_work: 0.2862 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 37674 Z= 0.198 Angle : 0.631 11.492 51115 Z= 0.317 Chirality : 0.046 0.174 5832 Planarity : 0.005 0.056 6628 Dihedral : 8.059 168.034 5271 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.80 % Favored : 96.18 % Rotamer: Outliers : 2.21 % Allowed : 9.97 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.34 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.12), residues: 4662 helix: 0.48 (0.12), residues: 1952 sheet: 0.06 (0.21), residues: 580 loop : -1.91 (0.12), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 275 TYR 0.023 0.001 TYR F 224 PHE 0.029 0.001 PHE C 466 TRP 0.017 0.001 TRP D 171 HIS 0.008 0.001 HIS D 454 Details of bonding type rmsd covalent geometry : bond 0.00477 (37674) covalent geometry : angle 0.63066 (51115) hydrogen bonds : bond 0.04697 ( 1500) hydrogen bonds : angle 4.63298 ( 4353) *********************** 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 331 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 244 time to evaluate : 1.504 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: B 230 MET cc_start: 0.6950 (mtm) cc_final: 0.6613 (mpp) REVERT: B 479 ARG cc_start: 0.8737 (mmp80) cc_final: 0.8405 (mpt180) REVERT: C 656 ASP cc_start: 0.9096 (p0) cc_final: 0.8801 (p0) REVERT: C 715 ILE cc_start: 0.9512 (OUTLIER) cc_final: 0.9226 (pp) REVERT: D 587 LYS cc_start: 0.8991 (pttt) cc_final: 0.8756 (pttm) REVERT: D 699 ASP cc_start: 0.8811 (t70) cc_final: 0.8459 (t0) REVERT: E 149 LEU cc_start: 0.3518 (OUTLIER) cc_final: 0.3076 (pt) REVERT: E 393 HIS cc_start: 0.6755 (OUTLIER) cc_final: 0.6095 (t-170) REVERT: E 441 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7732 (mm-30) REVERT: E 602 TRP cc_start: 0.8836 (t60) cc_final: 0.8630 (t60) REVERT: E 631 GLU cc_start: 0.8341 (mp0) cc_final: 0.7943 (mm-30) REVERT: F 324 ASP cc_start: 0.8290 (t0) cc_final: 0.7769 (OUTLIER) REVERT: F 328 ARG cc_start: 0.8703 (ttm110) cc_final: 0.8343 (ttm-80) REVERT: F 483 ASP cc_start: 0.8692 (m-30) cc_final: 0.8422 (p0) REVERT: F 541 ARG cc_start: 0.8083 (mmm-85) cc_final: 0.7609 (mtt-85) REVERT: A 47 VAL cc_start: -0.0750 (OUTLIER) cc_final: -0.1373 (p) REVERT: A 62 LEU cc_start: 0.1931 (OUTLIER) cc_final: 0.0979 (mp) REVERT: A 191 LYS cc_start: 0.5015 (OUTLIER) cc_final: 0.4517 (tppt) REVERT: A 246 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8110 (pt) REVERT: A 272 ARG cc_start: 0.7908 (pmm-80) cc_final: 0.7668 (pmm-80) REVERT: A 274 GLU cc_start: 0.9110 (tp30) cc_final: 0.8894 (mm-30) REVERT: A 656 ASP cc_start: 0.8932 (p0) cc_final: 0.8694 (p0) outliers start: 87 outliers final: 28 residues processed: 307 average time/residue: 0.8993 time to fit residues: 326.1181 Evaluate side-chains 263 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 674 LYS Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 385 ARG Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 452 THR Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 633 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 398 optimal weight: 50.0000 chunk 132 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 372 optimal weight: 5.9990 chunk 154 optimal weight: 60.0000 chunk 73 optimal weight: 2.9990 chunk 278 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 134 optimal weight: 0.0970 chunk 65 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 HIS ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 638 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.179553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106591 restraints weight = 65876.721| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.16 r_work: 0.2905 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37674 Z= 0.111 Angle : 0.558 9.193 51115 Z= 0.278 Chirality : 0.043 0.157 5832 Planarity : 0.004 0.053 6628 Dihedral : 7.789 165.401 5268 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.54 % Favored : 96.44 % Rotamer: Outliers : 1.73 % Allowed : 11.09 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.12), residues: 4662 helix: 1.00 (0.12), residues: 1943 sheet: 0.32 (0.22), residues: 561 loop : -1.68 (0.12), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 275 TYR 0.023 0.001 TYR F 224 PHE 0.013 0.001 PHE C 110 TRP 0.015 0.001 TRP D 171 HIS 0.008 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00253 (37674) covalent geometry : angle 0.55767 (51115) hydrogen bonds : bond 0.03565 ( 1500) hydrogen bonds : angle 4.28217 ( 4353) *********************** 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 321 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 253 time to evaluate : 1.553 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 230 MET cc_start: 0.7019 (mtm) cc_final: 0.6717 (mpp) REVERT: B 479 ARG cc_start: 0.8701 (mmp80) cc_final: 0.8456 (mpt180) REVERT: B 705 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8553 (tt0) REVERT: C 183 THR cc_start: 0.0919 (OUTLIER) cc_final: 0.0496 (p) REVERT: C 359 VAL cc_start: 0.7848 (OUTLIER) cc_final: 0.7638 (m) REVERT: C 656 ASP cc_start: 0.8960 (p0) cc_final: 0.8630 (p0) REVERT: D 587 LYS cc_start: 0.9045 (pttt) cc_final: 0.8828 (pttm) REVERT: D 699 ASP cc_start: 0.8585 (t70) cc_final: 0.8221 (t0) REVERT: D 748 LYS cc_start: 0.9102 (tppp) cc_final: 0.8786 (tppp) REVERT: E 144 LEU cc_start: -0.1165 (OUTLIER) cc_final: -0.1947 (mp) REVERT: E 149 LEU cc_start: 0.3541 (OUTLIER) cc_final: 0.3092 (pt) REVERT: E 328 ARG cc_start: 0.8018 (tpt170) cc_final: 0.7793 (tpt90) REVERT: E 346 ASN cc_start: 0.7887 (m-40) cc_final: 0.7424 (m-40) REVERT: E 389 GLU cc_start: 0.8065 (mp0) cc_final: 0.7626 (pm20) REVERT: E 393 HIS cc_start: 0.6477 (OUTLIER) cc_final: 0.5805 (t-170) REVERT: E 435 PRO cc_start: 0.7786 (Cg_endo) cc_final: 0.7563 (Cg_exo) REVERT: E 441 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7625 (mm-30) REVERT: E 489 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8256 (tm-30) REVERT: E 602 TRP cc_start: 0.8909 (t60) cc_final: 0.8588 (t60) REVERT: E 631 GLU cc_start: 0.8184 (mp0) cc_final: 0.7852 (mm-30) REVERT: F 483 ASP cc_start: 0.8593 (m-30) cc_final: 0.8387 (p0) REVERT: F 541 ARG cc_start: 0.7923 (mmm-85) cc_final: 0.7567 (mtt-85) REVERT: A 47 VAL cc_start: -0.1174 (OUTLIER) cc_final: -0.1598 (p) REVERT: A 62 LEU cc_start: 0.1651 (OUTLIER) cc_final: 0.0737 (mp) REVERT: A 191 LYS cc_start: 0.4971 (OUTLIER) cc_final: 0.4337 (mppt) REVERT: A 246 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8029 (pt) REVERT: A 274 GLU cc_start: 0.9075 (tp30) cc_final: 0.8834 (mm-30) REVERT: A 656 ASP cc_start: 0.8797 (p0) cc_final: 0.8564 (p0) outliers start: 68 outliers final: 23 residues processed: 304 average time/residue: 0.8758 time to fit residues: 315.6624 Evaluate side-chains 260 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 275 ARG Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 385 ARG Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 633 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 374 optimal weight: 0.2980 chunk 180 optimal weight: 5.9990 chunk 323 optimal weight: 0.7980 chunk 438 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 267 optimal weight: 8.9990 chunk 461 optimal weight: 0.9990 chunk 428 optimal weight: 7.9990 chunk 328 optimal weight: 6.9990 chunk 220 optimal weight: 0.6980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.178821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.103725 restraints weight = 66039.805| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.68 r_work: 0.2889 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37674 Z= 0.130 Angle : 0.569 13.266 51115 Z= 0.281 Chirality : 0.043 0.177 5832 Planarity : 0.004 0.053 6628 Dihedral : 7.656 162.951 5268 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.58 % Favored : 96.40 % Rotamer: Outliers : 1.98 % Allowed : 11.58 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.12), residues: 4662 helix: 1.29 (0.12), residues: 1937 sheet: 0.43 (0.21), residues: 586 loop : -1.54 (0.12), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 275 TYR 0.020 0.001 TYR F 224 PHE 0.016 0.001 PHE C 466 TRP 0.017 0.001 TRP D 602 HIS 0.005 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00307 (37674) covalent geometry : angle 0.56905 (51115) hydrogen bonds : bond 0.03697 ( 1500) hydrogen bonds : angle 4.16976 ( 4353) *********************** 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 317 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 239 time to evaluate : 1.549 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 479 ARG cc_start: 0.8756 (mmp80) cc_final: 0.8531 (mpt180) REVERT: B 649 GLN cc_start: 0.8945 (pp30) cc_final: 0.8704 (pp30) REVERT: B 705 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8785 (tt0) REVERT: C 183 THR cc_start: 0.0702 (OUTLIER) cc_final: 0.0259 (p) REVERT: C 323 LYS cc_start: 0.8565 (mtpm) cc_final: 0.8264 (mptt) REVERT: C 359 VAL cc_start: 0.7911 (OUTLIER) cc_final: 0.7656 (m) REVERT: C 656 ASP cc_start: 0.9109 (p0) cc_final: 0.8804 (p0) REVERT: D 587 LYS cc_start: 0.9022 (pttt) cc_final: 0.8792 (pttm) REVERT: D 699 ASP cc_start: 0.8660 (t70) cc_final: 0.8282 (t0) REVERT: E 144 LEU cc_start: -0.1268 (OUTLIER) cc_final: -0.2022 (mp) REVERT: E 149 LEU cc_start: 0.3471 (OUTLIER) cc_final: 0.3009 (pt) REVERT: E 393 HIS cc_start: 0.6674 (OUTLIER) cc_final: 0.5954 (t-170) REVERT: E 435 PRO cc_start: 0.7732 (Cg_endo) cc_final: 0.7469 (Cg_exo) REVERT: E 441 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7641 (mm-30) REVERT: E 602 TRP cc_start: 0.8891 (t60) cc_final: 0.8660 (t60) REVERT: E 631 GLU cc_start: 0.8319 (mp0) cc_final: 0.7913 (mm-30) REVERT: F 276 MET cc_start: 0.7574 (mmp) cc_final: 0.6112 (mtt) REVERT: F 324 ASP cc_start: 0.8725 (m-30) cc_final: 0.8124 (t0) REVERT: F 483 ASP cc_start: 0.8658 (m-30) cc_final: 0.8438 (p0) REVERT: F 486 GLU cc_start: 0.8915 (pt0) cc_final: 0.8255 (pm20) REVERT: F 541 ARG cc_start: 0.8086 (mmm-85) cc_final: 0.7680 (mtt-85) REVERT: A 47 VAL cc_start: -0.1183 (OUTLIER) cc_final: -0.1644 (p) REVERT: A 62 LEU cc_start: 0.1756 (OUTLIER) cc_final: 0.0832 (mp) REVERT: A 274 GLU cc_start: 0.9116 (tp30) cc_final: 0.8764 (mm-30) REVERT: A 656 ASP cc_start: 0.8932 (p0) cc_final: 0.8693 (p0) outliers start: 78 outliers final: 33 residues processed: 297 average time/residue: 0.8308 time to fit residues: 293.1597 Evaluate side-chains 268 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 275 ARG Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 385 ARG Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain F residue 258 MET Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 633 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 284 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 242 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 2 optimal weight: 50.0000 chunk 408 optimal weight: 40.0000 chunk 340 optimal weight: 9.9990 chunk 415 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 394 optimal weight: 30.0000 chunk 19 optimal weight: 40.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 148 GLN ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 HIS D 229 GLN D 309 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.175787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.099985 restraints weight = 65483.020| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.57 r_work: 0.2802 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 37674 Z= 0.310 Angle : 0.687 10.446 51115 Z= 0.342 Chirality : 0.049 0.192 5832 Planarity : 0.005 0.061 6628 Dihedral : 7.823 161.529 5268 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.93 % Favored : 96.05 % Rotamer: Outliers : 2.21 % Allowed : 12.19 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.12), residues: 4662 helix: 1.18 (0.12), residues: 1956 sheet: 0.47 (0.22), residues: 589 loop : -1.52 (0.12), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 275 TYR 0.021 0.002 TYR F 768 PHE 0.032 0.001 PHE C 466 TRP 0.019 0.002 TRP D 602 HIS 0.010 0.001 HIS D 454 Details of bonding type rmsd covalent geometry : bond 0.00766 (37674) covalent geometry : angle 0.68739 (51115) hydrogen bonds : bond 0.05318 ( 1500) hydrogen bonds : angle 4.49075 ( 4353) *********************** 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 337 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 250 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 423 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8250 (mt-10) REVERT: B 479 ARG cc_start: 0.8770 (mmp80) cc_final: 0.8472 (mpt180) REVERT: B 649 GLN cc_start: 0.8995 (pp30) cc_final: 0.8780 (pp30) REVERT: B 655 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8688 (mm-30) REVERT: C 252 LYS cc_start: 0.8949 (tttm) cc_final: 0.8610 (ttpp) REVERT: C 323 LYS cc_start: 0.8761 (mtpm) cc_final: 0.8502 (mptt) REVERT: C 656 ASP cc_start: 0.9134 (p0) cc_final: 0.8849 (p0) REVERT: C 715 ILE cc_start: 0.9510 (OUTLIER) cc_final: 0.9204 (pp) REVERT: D 496 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8220 (tmm) REVERT: D 587 LYS cc_start: 0.8983 (pttt) cc_final: 0.8751 (pttm) REVERT: D 699 ASP cc_start: 0.8810 (t70) cc_final: 0.8419 (t0) REVERT: E 144 LEU cc_start: -0.0139 (OUTLIER) cc_final: -0.0859 (mp) REVERT: E 149 LEU cc_start: 0.3536 (OUTLIER) cc_final: 0.3098 (pt) REVERT: E 393 HIS cc_start: 0.6730 (OUTLIER) cc_final: 0.6019 (t-170) REVERT: E 441 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7684 (mm-30) REVERT: E 516 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7346 (mmp) REVERT: E 602 TRP cc_start: 0.8948 (t60) cc_final: 0.8708 (t60) REVERT: E 631 GLU cc_start: 0.8422 (mp0) cc_final: 0.8133 (mm-30) REVERT: F 324 ASP cc_start: 0.8745 (m-30) cc_final: 0.8150 (t0) REVERT: F 486 GLU cc_start: 0.8880 (pt0) cc_final: 0.8192 (pm20) REVERT: F 541 ARG cc_start: 0.8279 (mmm-85) cc_final: 0.7685 (mtt-85) REVERT: A 47 VAL cc_start: -0.0830 (OUTLIER) cc_final: -0.1399 (p) REVERT: A 62 LEU cc_start: 0.1932 (OUTLIER) cc_final: 0.0992 (mp) REVERT: A 656 ASP cc_start: 0.8968 (p0) cc_final: 0.8765 (p0) outliers start: 87 outliers final: 47 residues processed: 308 average time/residue: 0.8827 time to fit residues: 321.4510 Evaluate side-chains 288 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 232 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 275 ARG Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 385 ARG Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 516 MET Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 258 MET Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain F residue 718 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 755 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 365 optimal weight: 2.9990 chunk 254 optimal weight: 10.0000 chunk 387 optimal weight: 5.9990 chunk 20 optimal weight: 50.0000 chunk 59 optimal weight: 1.9990 chunk 332 optimal weight: 0.0020 chunk 46 optimal weight: 0.9980 chunk 345 optimal weight: 0.8980 chunk 267 optimal weight: 2.9990 chunk 455 optimal weight: 8.9990 chunk 78 optimal weight: 50.0000 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 GLN ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.182477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.108152 restraints weight = 65495.313| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 4.22 r_work: 0.2822 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 37674 Z= 0.118 Angle : 0.576 10.683 51115 Z= 0.283 Chirality : 0.043 0.165 5832 Planarity : 0.004 0.057 6628 Dihedral : 7.680 161.251 5268 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.32 % Favored : 96.65 % Rotamer: Outliers : 1.78 % Allowed : 12.98 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.12), residues: 4662 helix: 1.45 (0.12), residues: 1949 sheet: 0.58 (0.22), residues: 586 loop : -1.38 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 275 TYR 0.018 0.001 TYR F 224 PHE 0.012 0.001 PHE C 467 TRP 0.021 0.001 TRP D 602 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00276 (37674) covalent geometry : angle 0.57628 (51115) hydrogen bonds : bond 0.03611 ( 1500) hydrogen bonds : angle 4.14184 ( 4353) *********************** 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 300 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 230 time to evaluate : 1.540 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 423 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8437 (mm-30) REVERT: B 479 ARG cc_start: 0.8733 (mmp80) cc_final: 0.8501 (mpt180) REVERT: B 649 GLN cc_start: 0.8871 (pp30) cc_final: 0.8633 (pp30) REVERT: B 655 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8549 (mm-30) REVERT: C 323 LYS cc_start: 0.8537 (mtpm) cc_final: 0.8305 (mptt) REVERT: C 449 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8251 (OUTLIER) REVERT: C 656 ASP cc_start: 0.9005 (p0) cc_final: 0.8684 (p0) REVERT: D 699 ASP cc_start: 0.8618 (t70) cc_final: 0.8182 (t0) REVERT: D 761 ASP cc_start: 0.8523 (m-30) cc_final: 0.8227 (t0) REVERT: E 75 MET cc_start: 0.2260 (pp-130) cc_final: 0.0015 (mmp) REVERT: E 144 LEU cc_start: -0.0524 (OUTLIER) cc_final: -0.1308 (mp) REVERT: E 149 LEU cc_start: 0.3532 (OUTLIER) cc_final: 0.3080 (pt) REVERT: E 393 HIS cc_start: 0.6606 (OUTLIER) cc_final: 0.5903 (t-170) REVERT: E 441 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7607 (mm-30) REVERT: E 516 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7140 (mmp) REVERT: E 602 TRP cc_start: 0.8941 (t60) cc_final: 0.8709 (t60) REVERT: E 631 GLU cc_start: 0.8228 (mp0) cc_final: 0.7983 (mm-30) REVERT: F 276 MET cc_start: 0.7416 (mmp) cc_final: 0.6019 (mtm) REVERT: F 324 ASP cc_start: 0.8687 (m-30) cc_final: 0.8078 (t0) REVERT: F 486 GLU cc_start: 0.8715 (pt0) cc_final: 0.8111 (pm20) REVERT: F 541 ARG cc_start: 0.8117 (mmm-85) cc_final: 0.7599 (mtt-85) REVERT: A 47 VAL cc_start: -0.1183 (OUTLIER) cc_final: -0.1639 (p) REVERT: A 62 LEU cc_start: 0.1861 (OUTLIER) cc_final: 0.0884 (mp) REVERT: A 656 ASP cc_start: 0.8871 (p0) cc_final: 0.8646 (p0) outliers start: 70 outliers final: 33 residues processed: 283 average time/residue: 0.8471 time to fit residues: 285.3451 Evaluate side-chains 267 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 227 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 385 ARG Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 516 MET Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 633 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 409 optimal weight: 9.9990 chunk 447 optimal weight: 5.9990 chunk 369 optimal weight: 0.7980 chunk 363 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 344 optimal weight: 5.9990 chunk 370 optimal weight: 8.9990 chunk 450 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 264 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.180695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.106608 restraints weight = 65553.424| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 4.04 r_work: 0.2804 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 37674 Z= 0.216 Angle : 0.629 12.569 51115 Z= 0.309 Chirality : 0.046 0.162 5832 Planarity : 0.004 0.059 6628 Dihedral : 7.654 160.259 5268 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.84 % Favored : 96.14 % Rotamer: Outliers : 1.83 % Allowed : 13.46 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.12), residues: 4662 helix: 1.46 (0.12), residues: 1949 sheet: 0.63 (0.22), residues: 582 loop : -1.33 (0.13), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 328 TYR 0.017 0.001 TYR F 224 PHE 0.022 0.001 PHE C 466 TRP 0.023 0.001 TRP D 602 HIS 0.007 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00529 (37674) covalent geometry : angle 0.62919 (51115) hydrogen bonds : bond 0.04446 ( 1500) hydrogen bonds : angle 4.23611 ( 4353) *********************** 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 305 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 233 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 479 ARG cc_start: 0.8763 (mmp80) cc_final: 0.8529 (mpt180) REVERT: B 649 GLN cc_start: 0.8892 (pp30) cc_final: 0.8685 (pp30) REVERT: C 323 LYS cc_start: 0.8657 (mtpm) cc_final: 0.8442 (mptt) REVERT: C 656 ASP cc_start: 0.8997 (p0) cc_final: 0.8648 (p0) REVERT: C 715 ILE cc_start: 0.9511 (OUTLIER) cc_final: 0.9158 (pp) REVERT: D 699 ASP cc_start: 0.8660 (t70) cc_final: 0.8266 (t0) REVERT: D 761 ASP cc_start: 0.8547 (m-30) cc_final: 0.8294 (t0) REVERT: E 75 MET cc_start: 0.2151 (pp-130) cc_final: -0.0066 (mmp) REVERT: E 144 LEU cc_start: -0.0483 (OUTLIER) cc_final: -0.1269 (mp) REVERT: E 149 LEU cc_start: 0.3492 (OUTLIER) cc_final: 0.3044 (pt) REVERT: E 393 HIS cc_start: 0.6727 (OUTLIER) cc_final: 0.6010 (t-170) REVERT: E 441 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7687 (mm-30) REVERT: E 489 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8260 (tm-30) REVERT: E 516 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7151 (mmp) REVERT: E 602 TRP cc_start: 0.8949 (t60) cc_final: 0.8729 (t60) REVERT: F 276 MET cc_start: 0.7474 (mmp) cc_final: 0.6035 (mtm) REVERT: F 324 ASP cc_start: 0.8661 (m-30) cc_final: 0.8057 (t0) REVERT: F 486 GLU cc_start: 0.8749 (pt0) cc_final: 0.8129 (pm20) REVERT: F 541 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.7650 (mtt-85) REVERT: A 47 VAL cc_start: -0.1387 (OUTLIER) cc_final: -0.1857 (p) REVERT: A 62 LEU cc_start: 0.1903 (OUTLIER) cc_final: 0.0950 (mp) REVERT: A 656 ASP cc_start: 0.8852 (p0) cc_final: 0.8619 (p0) outliers start: 72 outliers final: 48 residues processed: 288 average time/residue: 0.8507 time to fit residues: 292.7331 Evaluate side-chains 284 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 229 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 385 ARG Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 516 MET Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain F residue 258 MET Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain F residue 718 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 633 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 306 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 20 optimal weight: 50.0000 chunk 130 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 367 optimal weight: 2.9990 chunk 311 optimal weight: 50.0000 chunk 458 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 275 optimal weight: 9.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.178132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.104181 restraints weight = 65700.140| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.84 r_work: 0.2844 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37674 Z= 0.123 Angle : 0.589 13.883 51115 Z= 0.286 Chirality : 0.043 0.417 5832 Planarity : 0.004 0.057 6628 Dihedral : 7.566 159.425 5268 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.43 % Favored : 96.55 % Rotamer: Outliers : 1.42 % Allowed : 13.97 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.12), residues: 4662 helix: 1.60 (0.12), residues: 1952 sheet: 0.77 (0.22), residues: 565 loop : -1.22 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 275 TYR 0.019 0.001 TYR F 224 PHE 0.011 0.001 PHE C 466 TRP 0.025 0.001 TRP D 602 HIS 0.007 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00290 (37674) covalent geometry : angle 0.58903 (51115) hydrogen bonds : bond 0.03505 ( 1500) hydrogen bonds : angle 4.04432 ( 4353) *********************** 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 289 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 233 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 479 ARG cc_start: 0.8717 (mmp80) cc_final: 0.8493 (mpt180) REVERT: B 649 GLN cc_start: 0.8845 (pp30) cc_final: 0.8610 (pp30) REVERT: B 655 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8532 (mm-30) REVERT: C 323 LYS cc_start: 0.8498 (mtpm) cc_final: 0.8274 (mptt) REVERT: C 656 ASP cc_start: 0.8989 (p0) cc_final: 0.8668 (p0) REVERT: D 432 ARG cc_start: 0.8253 (ttt180) cc_final: 0.7973 (ttt90) REVERT: D 699 ASP cc_start: 0.8576 (t70) cc_final: 0.8135 (t0) REVERT: D 761 ASP cc_start: 0.8498 (m-30) cc_final: 0.8228 (t0) REVERT: E 75 MET cc_start: 0.1923 (pp-130) cc_final: -0.0391 (mmp) REVERT: E 144 LEU cc_start: -0.1352 (OUTLIER) cc_final: -0.2120 (mp) REVERT: E 149 LEU cc_start: 0.3510 (OUTLIER) cc_final: 0.3076 (pt) REVERT: E 393 HIS cc_start: 0.6490 (OUTLIER) cc_final: 0.5794 (t-170) REVERT: E 423 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7649 (mm-30) REVERT: E 441 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7686 (mm-30) REVERT: E 489 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8152 (tm-30) REVERT: E 516 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7011 (mmp) REVERT: E 602 TRP cc_start: 0.8972 (t60) cc_final: 0.8737 (t60) REVERT: F 276 MET cc_start: 0.7480 (mmp) cc_final: 0.6130 (mtm) REVERT: F 324 ASP cc_start: 0.8647 (m-30) cc_final: 0.8016 (t0) REVERT: F 486 GLU cc_start: 0.8649 (pt0) cc_final: 0.8142 (pm20) REVERT: F 541 ARG cc_start: 0.8057 (mmm-85) cc_final: 0.7573 (mtt-85) REVERT: A 47 VAL cc_start: -0.1534 (OUTLIER) cc_final: -0.1916 (p) REVERT: A 62 LEU cc_start: 0.1869 (OUTLIER) cc_final: 0.0889 (mp) REVERT: A 656 ASP cc_start: 0.8850 (p0) cc_final: 0.8637 (p0) outliers start: 56 outliers final: 36 residues processed: 276 average time/residue: 0.8537 time to fit residues: 281.6490 Evaluate side-chains 274 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 633 MET Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 385 ARG Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 516 MET Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 452 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 718 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 633 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 445 optimal weight: 0.4980 chunk 86 optimal weight: 4.9990 chunk 281 optimal weight: 4.9990 chunk 457 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 414 optimal weight: 4.9990 chunk 158 optimal weight: 30.0000 chunk 297 optimal weight: 0.8980 chunk 163 optimal weight: 40.0000 chunk 272 optimal weight: 8.9990 chunk 235 optimal weight: 8.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.177525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.103086 restraints weight = 65627.829| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.79 r_work: 0.2821 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 37674 Z= 0.162 Angle : 0.604 12.882 51115 Z= 0.295 Chirality : 0.044 0.437 5832 Planarity : 0.004 0.057 6628 Dihedral : 7.523 158.634 5268 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.69 % Favored : 96.29 % Rotamer: Outliers : 1.37 % Allowed : 14.10 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.12), residues: 4662 helix: 1.62 (0.12), residues: 1947 sheet: 0.81 (0.22), residues: 565 loop : -1.19 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 275 TYR 0.018 0.001 TYR F 224 PHE 0.016 0.001 PHE C 466 TRP 0.029 0.001 TRP D 602 HIS 0.008 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00393 (37674) covalent geometry : angle 0.60443 (51115) hydrogen bonds : bond 0.03875 ( 1500) hydrogen bonds : angle 4.08298 ( 4353) ********************** 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 287 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 233 time to evaluate : 1.513 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 479 ARG cc_start: 0.8749 (mmp80) cc_final: 0.8528 (mpt180) REVERT: B 649 GLN cc_start: 0.8859 (pp30) cc_final: 0.8650 (pp30) REVERT: B 655 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8525 (mm-30) REVERT: C 323 LYS cc_start: 0.8581 (mtpm) cc_final: 0.8360 (mptt) REVERT: C 656 ASP cc_start: 0.9004 (p0) cc_final: 0.8691 (p0) REVERT: D 432 ARG cc_start: 0.8219 (ttt180) cc_final: 0.7979 (ttt90) REVERT: D 587 LYS cc_start: 0.8989 (pttt) cc_final: 0.8773 (pttm) REVERT: D 699 ASP cc_start: 0.8571 (t70) cc_final: 0.8143 (t0) REVERT: D 761 ASP cc_start: 0.8538 (m-30) cc_final: 0.8276 (t0) REVERT: E 75 MET cc_start: 0.1945 (pp-130) cc_final: -0.0373 (mmp) REVERT: E 144 LEU cc_start: -0.1092 (OUTLIER) cc_final: -0.1869 (mp) REVERT: E 149 LEU cc_start: 0.3501 (OUTLIER) cc_final: 0.3074 (pt) REVERT: E 423 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7726 (mm-30) REVERT: E 441 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7712 (mm-30) REVERT: E 489 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8194 (tm-30) REVERT: E 516 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7017 (mmp) REVERT: E 602 TRP cc_start: 0.8966 (t60) cc_final: 0.8743 (t60) REVERT: F 276 MET cc_start: 0.7406 (mmp) cc_final: 0.6004 (mtm) REVERT: F 324 ASP cc_start: 0.8638 (m-30) cc_final: 0.8012 (t0) REVERT: F 486 GLU cc_start: 0.8649 (pt0) cc_final: 0.8156 (pm20) REVERT: F 541 ARG cc_start: 0.8117 (mmm-85) cc_final: 0.7616 (mtt-85) REVERT: A 47 VAL cc_start: -0.1505 (OUTLIER) cc_final: -0.1913 (p) REVERT: A 62 LEU cc_start: 0.1874 (OUTLIER) cc_final: 0.0903 (mp) REVERT: A 656 ASP cc_start: 0.8849 (p0) cc_final: 0.8634 (p0) outliers start: 54 outliers final: 42 residues processed: 273 average time/residue: 0.7847 time to fit residues: 254.9947 Evaluate side-chains 276 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 229 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 633 MET Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 385 ARG Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 516 MET Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 452 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 511 VAL Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain F residue 718 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 702 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 333 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 340 optimal weight: 1.9990 chunk 423 optimal weight: 9.9990 chunk 253 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 415 optimal weight: 0.9990 chunk 313 optimal weight: 0.4980 chunk 342 optimal weight: 6.9990 chunk 456 optimal weight: 4.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.177871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.104020 restraints weight = 65228.975| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 4.04 r_work: 0.2830 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 37674 Z= 0.145 Angle : 0.603 12.862 51115 Z= 0.294 Chirality : 0.044 0.425 5832 Planarity : 0.004 0.058 6628 Dihedral : 7.495 158.130 5268 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.32 % Allowed : 14.20 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.12), residues: 4662 helix: 1.63 (0.12), residues: 1949 sheet: 0.83 (0.22), residues: 565 loop : -1.16 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 275 TYR 0.017 0.001 TYR F 224 PHE 0.014 0.001 PHE C 466 TRP 0.028 0.001 TRP D 602 HIS 0.008 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00350 (37674) covalent geometry : angle 0.60317 (51115) hydrogen bonds : bond 0.03746 ( 1500) hydrogen bonds : angle 4.07181 ( 4353) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33565.85 seconds wall clock time: 566 minutes 26.81 seconds (33986.81 seconds total)