Starting phenix.real_space_refine on Fri Mar 6 17:44:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wpk_21863/03_2026/6wpk_21863.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wpk_21863/03_2026/6wpk_21863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wpk_21863/03_2026/6wpk_21863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wpk_21863/03_2026/6wpk_21863.map" model { file = "/net/cci-nas-00/data/ceres_data/6wpk_21863/03_2026/6wpk_21863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wpk_21863/03_2026/6wpk_21863.cif" } resolution = 3.3 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= 0.005 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: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 20917 2.51 5 N 6072 2.21 5 O 6104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33229 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4157 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 17, 'TRANS': 529} Chain breaks: 10 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 4, 'GLN:plan1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4155 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 17, 'TRANS': 529} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 4, 'GLN:plan1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4153 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 17, 'TRANS': 529} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 4, 'GLN:plan1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4153 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 17, 'TRANS': 529} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 4, 'GLN:plan1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "E" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4153 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 17, 'TRANS': 529} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 4, 'GLN:plan1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "F" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4153 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 17, 'TRANS': 529} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 4, 'GLN:plan1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "G" Number of atoms: 4152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4152 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 17, 'TRANS': 529} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 4, 'GLN:plan1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "H" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4153 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 17, 'TRANS': 529} Chain breaks: 10 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 4, 'GLN:plan1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Time building chain proxies: 7.46, per 1000 atoms: 0.22 Number of scatterers: 33229 At special positions: 0 Unit cell: (204.37, 204.37, 81.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 6104 8.00 N 6072 7.00 C 20917 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.4 seconds 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8112 Finding SS restraints... Secondary structure from input PDB file: 324 helices and 16 sheets defined 73.8% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 52 through 68 Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 128 through 135 removed outlier: 3.660A pdb=" N GLN A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 removed outlier: 3.531A pdb=" N LEU A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.609A pdb=" N ARG A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 177 through 192 removed outlier: 4.736A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.857A pdb=" N ALA A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.584A pdb=" N LEU A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 236 removed outlier: 3.596A pdb=" N ARG A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 230 " --> pdb=" O CYS A 226 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 248 removed outlier: 3.520A pdb=" N ARG A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 258 Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 265 through 280 removed outlier: 3.986A pdb=" N ASN A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 290 removed outlier: 3.831A pdb=" N SER A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 295 Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 323 through 329 Processing helix chain 'A' and resid 330 through 335 removed outlier: 3.846A pdb=" N LEU A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 359 removed outlier: 3.643A pdb=" N CYS A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.828A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 398 Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 413 through 425 removed outlier: 3.550A pdb=" N VAL A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 459 through 475 Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.666A pdb=" N CYS A 482 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP A 483 " --> pdb=" O SER A 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 483' Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.814A pdb=" N TRP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 494 " --> pdb=" O TRP A 490 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 removed outlier: 3.891A pdb=" N ARG A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 496 through 500' Processing helix chain 'A' and resid 501 through 508 removed outlier: 3.871A pdb=" N CYS A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.578A pdb=" N ARG A 517 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 531 through 543 removed outlier: 3.549A pdb=" N ALA A 541 " --> pdb=" O ARG A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 586 Processing helix chain 'A' and resid 605 through 614 removed outlier: 3.904A pdb=" N GLY A 613 " --> pdb=" O GLN A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 649 removed outlier: 4.258A pdb=" N CYS A 649 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 703 Processing helix chain 'B' and resid 52 through 68 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 105 through 115 removed outlier: 4.364A pdb=" N GLY B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 135 removed outlier: 3.515A pdb=" N GLN B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 149 Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.570A pdb=" N ARG B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE B 163 " --> pdb=" O ARG B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 177 through 192 removed outlier: 4.672A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 208 through 214 Processing helix chain 'B' and resid 219 through 236 removed outlier: 3.682A pdb=" N ARG B 224 " --> pdb=" O PRO B 220 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 230 " --> pdb=" O CYS B 226 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 248 removed outlier: 3.560A pdb=" N ARG B 243 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 265 through 280 removed outlier: 3.974A pdb=" N ASN B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 290 removed outlier: 3.876A pdb=" N SER B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 295 Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 323 through 329 Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.810A pdb=" N LEU B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 359 Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 369 through 380 removed outlier: 3.915A pdb=" N SER B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 398 removed outlier: 3.510A pdb=" N GLY B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 413 through 425 removed outlier: 3.617A pdb=" N VAL B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 440 through 445 Processing helix chain 'B' and resid 447 through 454 Processing helix chain 'B' and resid 459 through 475 removed outlier: 4.127A pdb=" N GLU B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 removed outlier: 3.760A pdb=" N TRP B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 494 " --> pdb=" O TRP B 490 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 removed outlier: 3.764A pdb=" N ARG B 499 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN B 500 " --> pdb=" O ARG B 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 496 through 500' Processing helix chain 'B' and resid 501 through 508 removed outlier: 3.818A pdb=" N CYS B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.736A pdb=" N VAL B 518 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 Processing helix chain 'B' and resid 531 through 544 removed outlier: 3.603A pdb=" N ALA B 541 " --> pdb=" O ARG B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 586 Processing helix chain 'B' and resid 605 through 614 removed outlier: 3.843A pdb=" N GLY B 613 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 644 removed outlier: 3.566A pdb=" N VAL B 644 " --> pdb=" O HIS B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 649 removed outlier: 4.384A pdb=" N CYS B 649 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 703 Processing helix chain 'C' and resid 52 through 68 Processing helix chain 'C' and resid 78 through 91 Processing helix chain 'C' and resid 105 through 115 removed outlier: 4.295A pdb=" N GLY C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 135 removed outlier: 3.516A pdb=" N GLN C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.543A pdb=" N LEU C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 163 removed outlier: 3.606A pdb=" N ARG C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE C 163 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 172 Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.551A pdb=" N ALA C 181 " --> pdb=" O PRO C 177 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.813A pdb=" N ALA C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C 205 " --> pdb=" O ARG C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 214 removed outlier: 3.611A pdb=" N LEU C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 217 No H-bonds generated for 'chain 'C' and resid 215 through 217' Processing helix chain 'C' and resid 219 through 236 removed outlier: 3.601A pdb=" N ARG C 224 " --> pdb=" O PRO C 220 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 230 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 248 removed outlier: 3.534A pdb=" N ARG C 243 " --> pdb=" O GLN C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 258 Proline residue: C 256 - end of helix Processing helix chain 'C' and resid 265 through 280 removed outlier: 4.005A pdb=" N ASN C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 290 removed outlier: 3.807A pdb=" N SER C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 295 Processing helix chain 'C' and resid 296 through 301 Processing helix chain 'C' and resid 323 through 329 Processing helix chain 'C' and resid 330 through 335 removed outlier: 3.868A pdb=" N LEU C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 359 removed outlier: 3.669A pdb=" N CYS C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.833A pdb=" N SER C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 398 Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 413 through 425 removed outlier: 3.555A pdb=" N VAL C 417 " --> pdb=" O LYS C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 436 Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 447 through 454 Processing helix chain 'C' and resid 459 through 475 Processing helix chain 'C' and resid 479 through 483 removed outlier: 3.668A pdb=" N CYS C 482 " --> pdb=" O TYR C 479 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP C 483 " --> pdb=" O SER C 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 479 through 483' Processing helix chain 'C' and resid 486 through 495 removed outlier: 3.814A pdb=" N TRP C 490 " --> pdb=" O ASN C 486 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU C 494 " --> pdb=" O TRP C 490 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 500 removed outlier: 3.879A pdb=" N ARG C 499 " --> pdb=" O PRO C 496 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN C 500 " --> pdb=" O ARG C 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 496 through 500' Processing helix chain 'C' and resid 501 through 508 removed outlier: 3.871A pdb=" N CYS C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 518 removed outlier: 3.739A pdb=" N VAL C 518 " --> pdb=" O LEU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 531 through 543 removed outlier: 3.559A pdb=" N ALA C 541 " --> pdb=" O ARG C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 586 Processing helix chain 'C' and resid 605 through 614 removed outlier: 3.904A pdb=" N GLY C 613 " --> pdb=" O GLN C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 649 removed outlier: 4.218A pdb=" N CYS C 649 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 703 Processing helix chain 'D' and resid 52 through 68 Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 105 through 115 removed outlier: 4.348A pdb=" N GLY D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 135 removed outlier: 3.514A pdb=" N GLN D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 149 Processing helix chain 'D' and resid 153 through 163 removed outlier: 3.574A pdb=" N ARG D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE D 163 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 172 Processing helix chain 'D' and resid 177 through 192 removed outlier: 3.624A pdb=" N ALA D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.880A pdb=" N ALA D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA D 205 " --> pdb=" O ARG D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 214 removed outlier: 3.509A pdb=" N LEU D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 217 No H-bonds generated for 'chain 'D' and resid 215 through 217' Processing helix chain 'D' and resid 219 through 236 removed outlier: 3.506A pdb=" N LEU D 223 " --> pdb=" O ASP D 219 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG D 224 " --> pdb=" O PRO D 220 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 230 " --> pdb=" O CYS D 226 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 248 removed outlier: 3.553A pdb=" N ARG D 243 " --> pdb=" O GLN D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 Processing helix chain 'D' and resid 265 through 280 removed outlier: 3.972A pdb=" N ASN D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 290 removed outlier: 3.877A pdb=" N SER D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 295 Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 323 through 329 Processing helix chain 'D' and resid 330 through 335 removed outlier: 3.832A pdb=" N LEU D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 359 Processing helix chain 'D' and resid 364 through 369 Processing helix chain 'D' and resid 369 through 380 removed outlier: 3.919A pdb=" N SER D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 398 Processing helix chain 'D' and resid 408 through 412 Processing helix chain 'D' and resid 413 through 425 removed outlier: 3.612A pdb=" N VAL D 417 " --> pdb=" O LYS D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 428 No H-bonds generated for 'chain 'D' and resid 426 through 428' Processing helix chain 'D' and resid 429 through 436 Processing helix chain 'D' and resid 440 through 445 Processing helix chain 'D' and resid 447 through 454 Processing helix chain 'D' and resid 459 through 475 Processing helix chain 'D' and resid 486 through 495 removed outlier: 3.761A pdb=" N TRP D 490 " --> pdb=" O ASN D 486 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU D 494 " --> pdb=" O TRP D 490 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 500 removed outlier: 3.763A pdb=" N ARG D 499 " --> pdb=" O PRO D 496 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN D 500 " --> pdb=" O ARG D 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 496 through 500' Processing helix chain 'D' and resid 501 through 508 removed outlier: 3.847A pdb=" N CYS D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 518 removed outlier: 3.731A pdb=" N VAL D 518 " --> pdb=" O LEU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 531 through 544 removed outlier: 3.604A pdb=" N ALA D 541 " --> pdb=" O ARG D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 586 Processing helix chain 'D' and resid 605 through 614 removed outlier: 3.841A pdb=" N GLY D 613 " --> pdb=" O GLN D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 644 removed outlier: 3.565A pdb=" N VAL D 644 " --> pdb=" O HIS D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 703 Processing helix chain 'E' and resid 52 through 68 Processing helix chain 'E' and resid 78 through 91 Processing helix chain 'E' and resid 105 through 115 removed outlier: 4.292A pdb=" N GLY E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 135 removed outlier: 3.515A pdb=" N GLN E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 149 removed outlier: 3.520A pdb=" N LEU E 147 " --> pdb=" O GLN E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 163 removed outlier: 3.601A pdb=" N ARG E 162 " --> pdb=" O ASP E 158 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE E 163 " --> pdb=" O ARG E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 172 Processing helix chain 'E' and resid 177 through 193 removed outlier: 4.632A pdb=" N SER E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 removed outlier: 3.866A pdb=" N ALA E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA E 205 " --> pdb=" O ARG E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 214 removed outlier: 3.624A pdb=" N LEU E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 217 No H-bonds generated for 'chain 'E' and resid 215 through 217' Processing helix chain 'E' and resid 219 through 236 removed outlier: 3.596A pdb=" N ARG E 224 " --> pdb=" O PRO E 220 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU E 228 " --> pdb=" O ARG E 224 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU E 230 " --> pdb=" O CYS E 226 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 248 removed outlier: 3.539A pdb=" N ARG E 243 " --> pdb=" O GLN E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 258 Proline residue: E 256 - end of helix Processing helix chain 'E' and resid 265 through 280 removed outlier: 3.976A pdb=" N ASN E 280 " --> pdb=" O VAL E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 290 removed outlier: 3.835A pdb=" N SER E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 295 Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 323 through 329 Processing helix chain 'E' and resid 330 through 335 removed outlier: 3.861A pdb=" N LEU E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 359 removed outlier: 3.642A pdb=" N CYS E 343 " --> pdb=" O LEU E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 380 removed outlier: 3.902A pdb=" N SER E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 398 Processing helix chain 'E' and resid 408 through 412 Processing helix chain 'E' and resid 413 through 425 removed outlier: 3.554A pdb=" N VAL E 417 " --> pdb=" O LYS E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 436 Processing helix chain 'E' and resid 440 through 445 Processing helix chain 'E' and resid 447 through 454 Processing helix chain 'E' and resid 459 through 475 Processing helix chain 'E' and resid 479 through 483 removed outlier: 3.667A pdb=" N CYS E 482 " --> pdb=" O TYR E 479 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP E 483 " --> pdb=" O SER E 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 479 through 483' Processing helix chain 'E' and resid 486 through 495 removed outlier: 3.819A pdb=" N TRP E 490 " --> pdb=" O ASN E 486 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU E 494 " --> pdb=" O TRP E 490 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP E 495 " --> pdb=" O LEU E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 500 removed outlier: 3.864A pdb=" N ARG E 499 " --> pdb=" O PRO E 496 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN E 500 " --> pdb=" O ARG E 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 496 through 500' Processing helix chain 'E' and resid 501 through 508 removed outlier: 3.868A pdb=" N CYS E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 518 removed outlier: 3.540A pdb=" N VAL E 518 " --> pdb=" O LEU E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 526 Processing helix chain 'E' and resid 531 through 543 removed outlier: 3.561A pdb=" N ALA E 541 " --> pdb=" O ARG E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 586 Processing helix chain 'E' and resid 605 through 614 removed outlier: 3.904A pdb=" N GLY E 613 " --> pdb=" O GLN E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 644 through 649 removed outlier: 4.252A pdb=" N CYS E 649 " --> pdb=" O THR E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 687 through 703 Processing helix chain 'F' and resid 52 through 68 Processing helix chain 'F' and resid 78 through 91 Processing helix chain 'F' and resid 105 through 116 removed outlier: 4.346A pdb=" N GLY F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 135 removed outlier: 3.803A pdb=" N GLN F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 149 Processing helix chain 'F' and resid 153 through 163 removed outlier: 3.558A pdb=" N ARG F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE F 163 " --> pdb=" O ARG F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 172 Processing helix chain 'F' and resid 177 through 192 removed outlier: 4.720A pdb=" N SER F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.854A pdb=" N ALA F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA F 205 " --> pdb=" O ARG F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 214 Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 219 through 236 removed outlier: 3.512A pdb=" N LEU F 223 " --> pdb=" O ASP F 219 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG F 224 " --> pdb=" O PRO F 220 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS F 225 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU F 230 " --> pdb=" O CYS F 226 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA F 234 " --> pdb=" O LEU F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 248 removed outlier: 3.559A pdb=" N ARG F 243 " --> pdb=" O GLN F 239 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG F 244 " --> pdb=" O ALA F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 255 Processing helix chain 'F' and resid 265 through 280 removed outlier: 3.974A pdb=" N ASN F 280 " --> pdb=" O VAL F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 290 removed outlier: 3.877A pdb=" N SER F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 295 Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 323 through 329 Processing helix chain 'F' and resid 330 through 335 removed outlier: 3.836A pdb=" N LEU F 334 " --> pdb=" O LEU F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 359 Processing helix chain 'F' and resid 364 through 369 Processing helix chain 'F' and resid 369 through 380 removed outlier: 3.914A pdb=" N SER F 373 " --> pdb=" O GLY F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 398 removed outlier: 3.517A pdb=" N GLY F 398 " --> pdb=" O LEU F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 412 Processing helix chain 'F' and resid 413 through 425 removed outlier: 3.611A pdb=" N VAL F 417 " --> pdb=" O LYS F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 428 No H-bonds generated for 'chain 'F' and resid 426 through 428' Processing helix chain 'F' and resid 429 through 436 Processing helix chain 'F' and resid 440 through 445 Processing helix chain 'F' and resid 447 through 454 Processing helix chain 'F' and resid 459 through 475 Processing helix chain 'F' and resid 486 through 495 removed outlier: 3.762A pdb=" N TRP F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU F 494 " --> pdb=" O TRP F 490 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 495 " --> pdb=" O LEU F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 500 removed outlier: 3.764A pdb=" N ARG F 499 " --> pdb=" O PRO F 496 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN F 500 " --> pdb=" O ARG F 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 496 through 500' Processing helix chain 'F' and resid 501 through 508 removed outlier: 3.788A pdb=" N CYS F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.733A pdb=" N VAL F 518 " --> pdb=" O LEU F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 526 Processing helix chain 'F' and resid 531 through 544 removed outlier: 3.605A pdb=" N ALA F 541 " --> pdb=" O ARG F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 586 Processing helix chain 'F' and resid 605 through 614 removed outlier: 3.833A pdb=" N GLY F 613 " --> pdb=" O GLN F 609 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 644 removed outlier: 3.571A pdb=" N VAL F 644 " --> pdb=" O HIS F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 687 through 703 Processing helix chain 'G' and resid 52 through 68 Processing helix chain 'G' and resid 78 through 91 Processing helix chain 'G' and resid 105 through 115 removed outlier: 4.327A pdb=" N GLY G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 135 removed outlier: 3.515A pdb=" N GLN G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA G 135 " --> pdb=" O ARG G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 149 removed outlier: 3.527A pdb=" N LEU G 147 " --> pdb=" O GLN G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 163 removed outlier: 3.592A pdb=" N ARG G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE G 163 " --> pdb=" O ARG G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 172 Processing helix chain 'G' and resid 177 through 192 removed outlier: 4.779A pdb=" N SER G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 removed outlier: 3.816A pdb=" N ALA G 204 " --> pdb=" O GLN G 200 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA G 205 " --> pdb=" O ARG G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 214 removed outlier: 3.656A pdb=" N LEU G 212 " --> pdb=" O LEU G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 219 through 236 removed outlier: 3.592A pdb=" N ARG G 224 " --> pdb=" O PRO G 220 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU G 228 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU G 230 " --> pdb=" O CYS G 226 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA G 234 " --> pdb=" O LEU G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 248 removed outlier: 3.534A pdb=" N ARG G 243 " --> pdb=" O GLN G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 258 Proline residue: G 256 - end of helix Processing helix chain 'G' and resid 265 through 280 removed outlier: 4.005A pdb=" N ASN G 280 " --> pdb=" O VAL G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 290 removed outlier: 3.822A pdb=" N SER G 290 " --> pdb=" O GLU G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 295 Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 323 through 329 Processing helix chain 'G' and resid 330 through 335 removed outlier: 3.852A pdb=" N LEU G 334 " --> pdb=" O LEU G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 359 removed outlier: 3.654A pdb=" N CYS G 343 " --> pdb=" O LEU G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 380 removed outlier: 3.855A pdb=" N SER G 373 " --> pdb=" O GLY G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 384 through 398 Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 413 through 425 removed outlier: 3.554A pdb=" N VAL G 417 " --> pdb=" O LYS G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 436 Processing helix chain 'G' and resid 440 through 445 Processing helix chain 'G' and resid 447 through 454 Processing helix chain 'G' and resid 459 through 475 Processing helix chain 'G' and resid 479 through 483 removed outlier: 3.634A pdb=" N CYS G 482 " --> pdb=" O TYR G 479 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP G 483 " --> pdb=" O SER G 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 479 through 483' Processing helix chain 'G' and resid 486 through 495 removed outlier: 3.813A pdb=" N TRP G 490 " --> pdb=" O ASN G 486 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU G 494 " --> pdb=" O TRP G 490 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP G 495 " --> pdb=" O LEU G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 500 removed outlier: 3.864A pdb=" N ARG G 499 " --> pdb=" O PRO G 496 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN G 500 " --> pdb=" O ARG G 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 496 through 500' Processing helix chain 'G' and resid 501 through 508 removed outlier: 3.868A pdb=" N CYS G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 518 removed outlier: 3.539A pdb=" N VAL G 518 " --> pdb=" O LEU G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 526 Processing helix chain 'G' and resid 531 through 544 removed outlier: 3.553A pdb=" N ALA G 541 " --> pdb=" O ARG G 537 " (cutoff:3.500A) Processing helix chain 'G' and resid 574 through 586 Processing helix chain 'G' and resid 605 through 614 removed outlier: 3.904A pdb=" N GLY G 613 " --> pdb=" O GLN G 609 " (cutoff:3.500A) Processing helix chain 'G' and resid 644 through 649 removed outlier: 4.255A pdb=" N CYS G 649 " --> pdb=" O THR G 645 " (cutoff:3.500A) Processing helix chain 'G' and resid 687 through 703 Processing helix chain 'H' and resid 52 through 68 Processing helix chain 'H' and resid 78 through 91 Processing helix chain 'H' and resid 105 through 115 removed outlier: 4.350A pdb=" N GLY H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 135 removed outlier: 3.866A pdb=" N GLN H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA H 135 " --> pdb=" O ARG H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 149 Processing helix chain 'H' and resid 153 through 163 removed outlier: 3.622A pdb=" N ARG H 162 " --> pdb=" O ASP H 158 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE H 163 " --> pdb=" O ARG H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 172 Processing helix chain 'H' and resid 177 through 192 removed outlier: 3.546A pdb=" N ALA H 181 " --> pdb=" O PRO H 177 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N SER H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 204 removed outlier: 3.907A pdb=" N ALA H 204 " --> pdb=" O GLN H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 214 Processing helix chain 'H' and resid 215 through 217 No H-bonds generated for 'chain 'H' and resid 215 through 217' Processing helix chain 'H' and resid 219 through 236 removed outlier: 3.680A pdb=" N ARG H 224 " --> pdb=" O PRO H 220 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU H 228 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU H 230 " --> pdb=" O CYS H 226 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA H 234 " --> pdb=" O LEU H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 248 removed outlier: 3.537A pdb=" N ARG H 243 " --> pdb=" O GLN H 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 255 Processing helix chain 'H' and resid 265 through 280 removed outlier: 3.920A pdb=" N ASN H 280 " --> pdb=" O VAL H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 290 removed outlier: 3.913A pdb=" N SER H 290 " --> pdb=" O GLU H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 295 Processing helix chain 'H' and resid 296 through 301 Processing helix chain 'H' and resid 323 through 329 Processing helix chain 'H' and resid 330 through 335 removed outlier: 3.813A pdb=" N LEU H 334 " --> pdb=" O LEU H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 359 Processing helix chain 'H' and resid 364 through 369 Processing helix chain 'H' and resid 369 through 380 removed outlier: 3.914A pdb=" N SER H 373 " --> pdb=" O GLY H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 398 removed outlier: 3.513A pdb=" N GLY H 398 " --> pdb=" O LEU H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 412 Processing helix chain 'H' and resid 413 through 425 removed outlier: 3.611A pdb=" N VAL H 417 " --> pdb=" O LYS H 413 " (cutoff:3.500A) Processing helix chain 'H' and resid 426 through 428 No H-bonds generated for 'chain 'H' and resid 426 through 428' Processing helix chain 'H' and resid 429 through 436 Processing helix chain 'H' and resid 440 through 445 Processing helix chain 'H' and resid 447 through 454 Processing helix chain 'H' and resid 459 through 475 Processing helix chain 'H' and resid 486 through 495 removed outlier: 3.772A pdb=" N TRP H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU H 494 " --> pdb=" O TRP H 490 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP H 495 " --> pdb=" O LEU H 491 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 500 removed outlier: 3.764A pdb=" N ARG H 499 " --> pdb=" O PRO H 496 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN H 500 " --> pdb=" O ARG H 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 496 through 500' Processing helix chain 'H' and resid 501 through 508 removed outlier: 3.796A pdb=" N CYS H 508 " --> pdb=" O GLY H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 514 through 518 removed outlier: 3.744A pdb=" N VAL H 518 " --> pdb=" O LEU H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 526 Processing helix chain 'H' and resid 531 through 544 removed outlier: 3.606A pdb=" N ALA H 541 " --> pdb=" O ARG H 537 " (cutoff:3.500A) Processing helix chain 'H' and resid 574 through 586 Processing helix chain 'H' and resid 605 through 614 removed outlier: 3.794A pdb=" N GLY H 613 " --> pdb=" O GLN H 609 " (cutoff:3.500A) Processing helix chain 'H' and resid 639 through 644 removed outlier: 3.569A pdb=" N VAL H 644 " --> pdb=" O HIS H 640 " (cutoff:3.500A) Processing helix chain 'H' and resid 644 through 649 removed outlier: 4.385A pdb=" N CYS H 649 " --> pdb=" O THR H 645 " (cutoff:3.500A) Processing helix chain 'H' and resid 687 through 703 Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 567 removed outlier: 6.171A pdb=" N PHE A 565 " --> pdb=" O VAL A 618 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A 620 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER A 567 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 564 through 567 removed outlier: 6.171A pdb=" N PHE A 565 " --> pdb=" O VAL A 618 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A 620 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER A 567 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE A 656 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 619 " --> pdb=" O ILE A 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 566 through 568 removed outlier: 6.432A pdb=" N SER B 567 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 566 through 568 removed outlier: 6.432A pdb=" N SER B 567 " --> pdb=" O VAL B 620 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE B 656 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 619 " --> pdb=" O ILE B 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 564 through 567 removed outlier: 6.172A pdb=" N PHE C 565 " --> pdb=" O VAL C 618 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL C 620 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N SER C 567 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 564 through 567 removed outlier: 6.172A pdb=" N PHE C 565 " --> pdb=" O VAL C 618 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL C 620 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N SER C 567 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE C 656 " --> pdb=" O PHE C 617 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 619 " --> pdb=" O ILE C 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 566 through 568 removed outlier: 6.434A pdb=" N SER D 567 " --> pdb=" O VAL D 620 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 566 through 568 removed outlier: 6.434A pdb=" N SER D 567 " --> pdb=" O VAL D 620 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE D 656 " --> pdb=" O PHE D 617 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU D 619 " --> pdb=" O ILE D 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 564 through 567 removed outlier: 6.171A pdb=" N PHE E 565 " --> pdb=" O VAL E 618 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL E 620 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N SER E 567 " --> pdb=" O VAL E 620 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 564 through 567 removed outlier: 6.171A pdb=" N PHE E 565 " --> pdb=" O VAL E 618 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL E 620 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N SER E 567 " --> pdb=" O VAL E 620 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE E 656 " --> pdb=" O PHE E 617 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU E 619 " --> pdb=" O ILE E 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 566 through 568 removed outlier: 6.432A pdb=" N SER F 567 " --> pdb=" O VAL F 620 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 566 through 568 removed outlier: 6.432A pdb=" N SER F 567 " --> pdb=" O VAL F 620 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE F 656 " --> pdb=" O PHE F 617 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU F 619 " --> pdb=" O ILE F 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'G' and resid 564 through 567 removed outlier: 6.174A pdb=" N PHE G 565 " --> pdb=" O VAL G 618 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL G 620 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N SER G 567 " --> pdb=" O VAL G 620 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 564 through 567 removed outlier: 6.174A pdb=" N PHE G 565 " --> pdb=" O VAL G 618 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL G 620 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N SER G 567 " --> pdb=" O VAL G 620 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE G 656 " --> pdb=" O PHE G 617 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU G 619 " --> pdb=" O ILE G 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'H' and resid 566 through 568 removed outlier: 6.432A pdb=" N SER H 567 " --> pdb=" O VAL H 620 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 566 through 568 removed outlier: 6.432A pdb=" N SER H 567 " --> pdb=" O VAL H 620 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE H 656 " --> pdb=" O PHE H 617 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU H 619 " --> pdb=" O ILE H 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 1722 hydrogen bonds defined for protein. 5022 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: 6.22 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.52: 24631 1.52 - 1.82: 9022 1.82 - 2.11: 0 2.11 - 2.41: 0 2.41 - 2.71: 6 Bond restraints: 33659 Sorted by residual: bond pdb=" C LEU D 116 " pdb=" N ASP D 127 " ideal model delta sigma weight residual 1.328 2.700 -1.373 1.13e-02 7.83e+03 1.48e+04 bond pdb=" C LEU B 116 " pdb=" N ASP B 127 " ideal model delta sigma weight residual 1.332 2.705 -1.373 1.40e-02 5.10e+03 9.61e+03 bond pdb=" C LEU G 116 " pdb=" N ASP G 127 " ideal model delta sigma weight residual 1.332 2.638 -1.306 1.40e-02 5.10e+03 8.70e+03 bond pdb=" C LEU E 116 " pdb=" N ASP E 127 " ideal model delta sigma weight residual 1.332 2.623 -1.290 1.40e-02 5.10e+03 8.49e+03 bond pdb=" C LEU C 116 " pdb=" N ASP C 127 " ideal model delta sigma weight residual 1.332 2.621 -1.289 1.40e-02 5.10e+03 8.47e+03 ... (remaining 33654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.23: 45400 10.23 - 20.47: 0 20.47 - 30.70: 0 30.70 - 40.93: 5 40.93 - 51.17: 13 Bond angle restraints: 45418 Sorted by residual: angle pdb=" O LEU G 116 " pdb=" C LEU G 116 " pdb=" N ASP G 127 " ideal model delta sigma weight residual 123.34 173.36 -50.02 1.37e+00 5.33e-01 1.33e+03 angle pdb=" O LEU C 116 " pdb=" C LEU C 116 " pdb=" N ASP C 127 " ideal model delta sigma weight residual 123.34 173.13 -49.79 1.37e+00 5.33e-01 1.32e+03 angle pdb=" O LEU E 116 " pdb=" C LEU E 116 " pdb=" N ASP E 127 " ideal model delta sigma weight residual 123.34 173.09 -49.75 1.37e+00 5.33e-01 1.32e+03 angle pdb=" CA LEU E 116 " pdb=" C LEU E 116 " pdb=" N ASP E 127 " ideal model delta sigma weight residual 116.50 65.33 51.17 1.44e+00 4.82e-01 1.26e+03 angle pdb=" CA LEU C 116 " pdb=" C LEU C 116 " pdb=" N ASP C 127 " ideal model delta sigma weight residual 116.50 65.45 51.05 1.44e+00 4.82e-01 1.26e+03 ... (remaining 45413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18023 17.98 - 35.95: 1938 35.95 - 53.93: 355 53.93 - 71.91: 81 71.91 - 89.88: 19 Dihedral angle restraints: 20416 sinusoidal: 7938 harmonic: 12478 Sorted by residual: dihedral pdb=" CA LEU F 116 " pdb=" C LEU F 116 " pdb=" N ASP F 127 " pdb=" CA ASP F 127 " ideal model delta harmonic sigma weight residual 180.00 109.54 70.46 0 5.00e+00 4.00e-02 1.99e+02 dihedral pdb=" CA LEU D 116 " pdb=" C LEU D 116 " pdb=" N ASP D 127 " pdb=" CA ASP D 127 " ideal model delta harmonic sigma weight residual 180.00 153.16 26.84 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA LEU B 116 " pdb=" C LEU B 116 " pdb=" N ASP B 127 " pdb=" CA ASP B 127 " ideal model delta harmonic sigma weight residual 180.00 156.01 23.99 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 20413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4708 0.063 - 0.125: 560 0.125 - 0.188: 19 0.188 - 0.251: 4 0.251 - 0.314: 8 Chirality restraints: 5299 Sorted by residual: chirality pdb=" CA LEU B 303 " pdb=" N LEU B 303 " pdb=" C LEU B 303 " pdb=" CB LEU B 303 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA LEU F 303 " pdb=" N LEU F 303 " pdb=" C LEU F 303 " pdb=" CB LEU F 303 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA LEU D 303 " pdb=" N LEU D 303 " pdb=" C LEU D 303 " pdb=" CB LEU D 303 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 5296 not shown) Planarity restraints: 5862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 561 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO F 562 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO F 562 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 562 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 561 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO B 562 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 562 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 562 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR H 561 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO H 562 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO H 562 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 562 " -0.032 5.00e-02 4.00e+02 ... (remaining 5859 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 8778 2.80 - 3.33: 31009 3.33 - 3.85: 50181 3.85 - 4.38: 60932 4.38 - 4.90: 104706 Nonbonded interactions: 255606 Sorted by model distance: nonbonded pdb=" OG SER E 567 " pdb=" OE1 GLU E 642 " model vdw 2.277 3.040 nonbonded pdb=" OG SER A 567 " pdb=" OE1 GLU A 642 " model vdw 2.278 3.040 nonbonded pdb=" OG SER G 567 " pdb=" OE1 GLU G 642 " model vdw 2.278 3.040 nonbonded pdb=" NH2 ARG G 376 " pdb=" OE2 GLU G 472 " model vdw 2.280 3.120 nonbonded pdb=" NH2 ARG E 376 " pdb=" OE2 GLU E 472 " model vdw 2.280 3.120 ... (remaining 255601 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 51 through 87 or (resid 88 and (name N or name CA or name \ C or name O or name CB )) or (resid 89 through 108 and (name N or name CA or nam \ e C or name O or name CB )) or resid 109 through 544 or (resid 545 and (name N o \ r name CA or name C or name O or name CB or name CG or name SD )) or resid 561 t \ hrough 703)) selection = (chain 'B' and (resid 51 through 87 or (resid 88 and (name N or name CA or name \ C or name O or name CB )) or resid 89 through 544 or (resid 545 and (name N or n \ ame CA or name C or name O or name CB or name CG or name SD )) or resid 561 thro \ ugh 703)) selection = (chain 'C' and (resid 51 through 544 or (resid 545 and (name N or name CA or nam \ e C or name O or name CB or name CG or name SD )) or resid 561 through 703)) selection = (chain 'D' and (resid 51 through 544 or (resid 545 and (name N or name CA or nam \ e C or name O or name CB or name CG or name SD )) or resid 561 through 703)) selection = (chain 'E' and (resid 51 through 544 or (resid 545 and (name N or name CA or nam \ e C or name O or name CB or name CG or name SD )) or resid 561 through 703)) selection = (chain 'F' and (resid 51 through 544 or (resid 545 and (name N or name CA or nam \ e C or name O or name CB or name CG or name SD )) or resid 561 through 703)) selection = chain 'G' selection = (chain 'H' and (resid 51 through 544 or (resid 545 and (name N or name CA or nam \ e C or name O or name CB or name CG or name SD )) or resid 561 through 703)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 28.780 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.018 1.373 33659 Z= 1.339 Angle : 1.130 51.168 45418 Z= 0.717 Chirality : 0.043 0.314 5299 Planarity : 0.004 0.058 5862 Dihedral : 15.336 89.883 12304 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.65 % Allowed : 8.51 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.81 (0.11), residues: 4200 helix: -2.06 (0.09), residues: 2888 sheet: -3.55 (0.32), residues: 104 loop : -3.17 (0.15), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.008 0.001 TYR C 503 PHE 0.011 0.001 PHE A 617 TRP 0.006 0.001 TRP G 490 HIS 0.006 0.001 HIS G 236 Details of bonding type rmsd covalent geometry : bond 0.01843 (33659) covalent geometry : angle 1.12954 (45418) hydrogen bonds : bond 0.16247 ( 1722) hydrogen bonds : angle 5.88413 ( 5022) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 364 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 641 LYS cc_start: 0.6299 (OUTLIER) cc_final: 0.5952 (mtmt) REVERT: B 642 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7113 (pt0) REVERT: C 641 LYS cc_start: 0.6265 (OUTLIER) cc_final: 0.5929 (mtmt) REVERT: D 642 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7106 (pt0) REVERT: E 641 LYS cc_start: 0.6331 (OUTLIER) cc_final: 0.5968 (mtmt) REVERT: F 217 ARG cc_start: 0.7812 (mmt90) cc_final: 0.7421 (mmm-85) REVERT: G 217 ARG cc_start: 0.8174 (mmm160) cc_final: 0.7937 (mmp80) REVERT: G 641 LYS cc_start: 0.6283 (OUTLIER) cc_final: 0.5943 (mtmt) outliers start: 22 outliers final: 6 residues processed: 386 average time/residue: 0.2599 time to fit residues: 148.9016 Evaluate side-chains 264 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 252 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 642 GLU Chi-restraints excluded: chain C residue 641 LYS Chi-restraints excluded: chain C residue 642 GLU Chi-restraints excluded: chain D residue 642 GLU Chi-restraints excluded: chain E residue 641 LYS Chi-restraints excluded: chain E residue 642 GLU Chi-restraints excluded: chain F residue 642 GLU Chi-restraints excluded: chain G residue 641 LYS Chi-restraints excluded: chain G residue 642 GLU Chi-restraints excluded: chain H residue 642 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN A 239 GLN A 342 GLN A 383 ASN A 423 GLN A 436 GLN A 522 GLN A 587 HIS A 640 HIS A 700 GLN B 143 GLN B 239 GLN B 342 GLN B 383 ASN B 423 GLN B 436 GLN B 522 GLN B 587 HIS B 640 HIS B 700 GLN C 143 GLN C 200 GLN C 239 GLN C 342 GLN C 423 GLN C 436 GLN C 522 GLN C 587 HIS C 700 GLN D 143 GLN D 239 GLN D 342 GLN D 383 ASN D 423 GLN D 436 GLN D 522 GLN D 587 HIS D 640 HIS D 700 GLN E 143 GLN E 200 GLN E 239 GLN E 342 GLN E 383 ASN E 423 GLN E 436 GLN E 522 GLN E 587 HIS E 640 HIS E 700 GLN F 143 GLN F 239 GLN F 342 GLN F 383 ASN F 423 GLN F 436 GLN F 522 GLN F 587 HIS F 640 HIS F 700 GLN G 143 GLN G 200 GLN G 239 GLN G 342 GLN G 383 ASN G 423 GLN G 436 GLN G 522 GLN G 587 HIS G 640 HIS G 700 GLN H 143 GLN H 239 GLN H 342 GLN H 383 ASN H 423 GLN H 436 GLN H 522 GLN H 587 HIS H 640 HIS H 700 GLN Total number of N/Q/H flips: 81 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.160957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.105820 restraints weight = 46276.650| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.84 r_work: 0.3012 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 33659 Z= 0.207 Angle : 0.660 11.167 45418 Z= 0.324 Chirality : 0.041 0.173 5299 Planarity : 0.005 0.056 5862 Dihedral : 5.735 58.117 4750 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.98 % Favored : 92.00 % Rotamer: Outliers : 1.37 % Allowed : 15.53 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.12), residues: 4212 helix: -0.92 (0.09), residues: 2934 sheet: -2.56 (0.34), residues: 104 loop : -2.69 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 376 TYR 0.011 0.002 TYR D 687 PHE 0.019 0.001 PHE A 617 TRP 0.004 0.001 TRP G 490 HIS 0.005 0.001 HIS G 236 Details of bonding type rmsd covalent geometry : bond 0.00502 (33659) covalent geometry : angle 0.65961 (45418) hydrogen bonds : bond 0.04600 ( 1722) hydrogen bonds : angle 4.14692 ( 5022) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 269 time to evaluate : 1.303 Fit side-chains REVERT: B 399 GLU cc_start: 0.8292 (mp0) cc_final: 0.7649 (tt0) REVERT: B 642 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7628 (pt0) REVERT: C 153 VAL cc_start: 0.8311 (t) cc_final: 0.7941 (m) REVERT: D 642 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7582 (pt0) REVERT: E 153 VAL cc_start: 0.8327 (t) cc_final: 0.7963 (m) REVERT: F 217 ARG cc_start: 0.8289 (mmt90) cc_final: 0.7978 (mmp80) REVERT: F 642 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7552 (pt0) REVERT: G 217 ARG cc_start: 0.8335 (mmm160) cc_final: 0.8041 (mmp80) REVERT: H 642 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7610 (pt0) outliers start: 46 outliers final: 21 residues processed: 302 average time/residue: 0.2052 time to fit residues: 101.3476 Evaluate side-chains 270 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 245 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 642 GLU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 642 GLU Chi-restraints excluded: chain E residue 383 ASN Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 642 GLU Chi-restraints excluded: chain G residue 173 LYS Chi-restraints excluded: chain G residue 264 GLU Chi-restraints excluded: chain G residue 383 ASN Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 371 ILE Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 642 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 185 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 250 optimal weight: 2.9990 chunk 295 optimal weight: 0.7980 chunk 333 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 251 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 419 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.163616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108862 restraints weight = 45980.917| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.86 r_work: 0.3065 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33659 Z= 0.119 Angle : 0.594 12.488 45418 Z= 0.286 Chirality : 0.038 0.202 5299 Planarity : 0.004 0.048 5862 Dihedral : 4.700 36.111 4722 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.23 % Allowed : 15.85 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.13), residues: 4212 helix: -0.26 (0.10), residues: 2976 sheet: -1.69 (0.42), residues: 104 loop : -2.40 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 338 TYR 0.009 0.001 TYR F 687 PHE 0.018 0.001 PHE G 617 TRP 0.007 0.001 TRP C 490 HIS 0.002 0.000 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00275 (33659) covalent geometry : angle 0.59356 (45418) hydrogen bonds : bond 0.03546 ( 1722) hydrogen bonds : angle 3.67565 ( 5022) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 291 time to evaluate : 0.813 Fit side-chains REVERT: A 147 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6412 (mm) REVERT: A 489 ASP cc_start: 0.8907 (m-30) cc_final: 0.8661 (m-30) REVERT: A 656 ILE cc_start: 0.7471 (mt) cc_final: 0.7123 (tt) REVERT: B 330 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8683 (mp) REVERT: B 399 GLU cc_start: 0.8393 (mp0) cc_final: 0.7491 (tt0) REVERT: C 147 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6171 (mm) REVERT: C 244 ARG cc_start: 0.8196 (tpt170) cc_final: 0.7966 (mmm160) REVERT: D 147 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6038 (mm) REVERT: D 330 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8689 (mp) REVERT: D 399 GLU cc_start: 0.8338 (mp0) cc_final: 0.7250 (tt0) REVERT: E 147 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6407 (mm) REVERT: E 489 ASP cc_start: 0.8867 (m-30) cc_final: 0.8620 (m-30) REVERT: E 656 ILE cc_start: 0.7301 (mt) cc_final: 0.6971 (tt) REVERT: F 217 ARG cc_start: 0.8213 (mmt90) cc_final: 0.7717 (mmm-85) REVERT: F 330 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8692 (mp) REVERT: F 399 GLU cc_start: 0.7293 (tt0) cc_final: 0.6603 (tt0) REVERT: G 147 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6410 (mm) REVERT: G 217 ARG cc_start: 0.8306 (mmm160) cc_final: 0.7958 (mmp80) REVERT: G 244 ARG cc_start: 0.8186 (tpt170) cc_final: 0.7958 (mmm160) REVERT: G 489 ASP cc_start: 0.8870 (m-30) cc_final: 0.8611 (m-30) REVERT: H 330 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8687 (mp) REVERT: H 399 GLU cc_start: 0.7533 (tt0) cc_final: 0.7178 (tt0) outliers start: 75 outliers final: 26 residues processed: 336 average time/residue: 0.2078 time to fit residues: 113.5802 Evaluate side-chains 292 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 257 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 264 GLU Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 618 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 162 optimal weight: 70.0000 chunk 165 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 chunk 71 optimal weight: 0.0020 chunk 127 optimal weight: 0.7980 chunk 327 optimal weight: 4.9990 chunk 166 optimal weight: 20.0000 chunk 249 optimal weight: 0.9980 chunk 348 optimal weight: 7.9990 chunk 363 optimal weight: 7.9990 overall best weight: 2.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 ASN A 516 HIS E 383 ASN G 383 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.162945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108591 restraints weight = 45883.700| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.24 r_work: 0.3011 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 33659 Z= 0.150 Angle : 0.601 12.747 45418 Z= 0.289 Chirality : 0.039 0.182 5299 Planarity : 0.004 0.045 5862 Dihedral : 4.466 19.609 4710 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.32 % Allowed : 17.25 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 4212 helix: 0.02 (0.10), residues: 2976 sheet: -1.65 (0.39), residues: 104 loop : -2.22 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 543 TYR 0.009 0.001 TYR F 687 PHE 0.016 0.001 PHE E 617 TRP 0.003 0.001 TRP C 490 HIS 0.003 0.001 HIS G 236 Details of bonding type rmsd covalent geometry : bond 0.00361 (33659) covalent geometry : angle 0.60059 (45418) hydrogen bonds : bond 0.03753 ( 1722) hydrogen bonds : angle 3.57041 ( 5022) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 251 time to evaluate : 1.287 Fit side-chains REVERT: A 147 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6406 (mm) REVERT: A 489 ASP cc_start: 0.8756 (m-30) cc_final: 0.8533 (m-30) REVERT: B 330 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8663 (mp) REVERT: B 399 GLU cc_start: 0.8312 (mp0) cc_final: 0.7491 (tt0) REVERT: C 147 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6365 (mm) REVERT: C 244 ARG cc_start: 0.8112 (tpt170) cc_final: 0.7899 (mmm160) REVERT: D 143 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6654 (tt0) REVERT: D 147 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.6149 (mm) REVERT: D 330 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8675 (mp) REVERT: D 489 ASP cc_start: 0.8731 (m-30) cc_final: 0.8064 (m-30) REVERT: E 147 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6311 (mm) REVERT: E 489 ASP cc_start: 0.8734 (m-30) cc_final: 0.8510 (m-30) REVERT: E 656 ILE cc_start: 0.7425 (mt) cc_final: 0.7159 (tt) REVERT: F 147 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6066 (mm) REVERT: F 217 ARG cc_start: 0.8134 (mmt90) cc_final: 0.7653 (mmm-85) REVERT: F 330 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8669 (mp) REVERT: F 399 GLU cc_start: 0.7185 (tt0) cc_final: 0.6507 (tt0) REVERT: G 147 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6324 (mm) REVERT: G 217 ARG cc_start: 0.8257 (mmm160) cc_final: 0.7898 (mmp80) REVERT: G 244 ARG cc_start: 0.8111 (tpt170) cc_final: 0.7894 (mmm160) REVERT: G 489 ASP cc_start: 0.8748 (m-30) cc_final: 0.8509 (m-30) REVERT: H 330 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8668 (mp) REVERT: H 399 GLU cc_start: 0.7418 (tt0) cc_final: 0.7157 (tt0) outliers start: 78 outliers final: 39 residues processed: 308 average time/residue: 0.2080 time to fit residues: 103.2967 Evaluate side-chains 297 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 247 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 383 ASN Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 593 ILE Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 383 ASN Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 618 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 199 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 chunk 341 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 274 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 430 optimal weight: 0.3980 chunk 222 optimal weight: 7.9990 chunk 174 optimal weight: 0.0980 chunk 122 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.165208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110436 restraints weight = 45905.112| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.86 r_work: 0.3079 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 33659 Z= 0.101 Angle : 0.563 12.740 45418 Z= 0.267 Chirality : 0.037 0.174 5299 Planarity : 0.003 0.041 5862 Dihedral : 4.222 18.965 4710 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.35 % Allowed : 17.49 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.13), residues: 4212 helix: 0.45 (0.10), residues: 2926 sheet: -1.42 (0.40), residues: 104 loop : -1.95 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 543 TYR 0.007 0.001 TYR B 687 PHE 0.014 0.001 PHE G 617 TRP 0.005 0.001 TRP C 490 HIS 0.002 0.000 HIS G 236 Details of bonding type rmsd covalent geometry : bond 0.00228 (33659) covalent geometry : angle 0.56290 (45418) hydrogen bonds : bond 0.03078 ( 1722) hydrogen bonds : angle 3.36343 ( 5022) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 258 time to evaluate : 1.319 Fit side-chains REVERT: A 147 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6287 (mm) REVERT: A 489 ASP cc_start: 0.8892 (m-30) cc_final: 0.8689 (m-30) REVERT: B 330 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8643 (mp) REVERT: B 399 GLU cc_start: 0.8296 (mp0) cc_final: 0.7317 (tt0) REVERT: B 489 ASP cc_start: 0.8885 (m-30) cc_final: 0.8329 (m-30) REVERT: C 147 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6219 (mm) REVERT: D 143 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6675 (tt0) REVERT: D 147 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6159 (mm) REVERT: D 330 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8629 (mp) REVERT: D 489 ASP cc_start: 0.8902 (m-30) cc_final: 0.8436 (m-30) REVERT: E 147 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.6117 (mm) REVERT: E 248 LYS cc_start: 0.8260 (mttt) cc_final: 0.8028 (mtmt) REVERT: E 489 ASP cc_start: 0.8871 (m-30) cc_final: 0.8667 (m-30) REVERT: F 147 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6154 (mm) REVERT: F 217 ARG cc_start: 0.8175 (mmt90) cc_final: 0.7568 (mmm-85) REVERT: F 330 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8618 (mp) REVERT: F 399 GLU cc_start: 0.7102 (tt0) cc_final: 0.6546 (tt0) REVERT: F 489 ASP cc_start: 0.8865 (m-30) cc_final: 0.8303 (m-30) REVERT: G 147 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6223 (mm) REVERT: G 217 ARG cc_start: 0.8241 (mmm160) cc_final: 0.7722 (mmt-90) REVERT: G 489 ASP cc_start: 0.8869 (m-30) cc_final: 0.8652 (m-30) REVERT: H 330 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8656 (mp) REVERT: H 399 GLU cc_start: 0.7306 (tt0) cc_final: 0.6701 (tt0) REVERT: H 489 ASP cc_start: 0.8874 (m-30) cc_final: 0.8319 (m-30) outliers start: 79 outliers final: 42 residues processed: 311 average time/residue: 0.1969 time to fit residues: 99.8346 Evaluate side-chains 294 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 241 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 593 ILE Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 593 ILE Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 618 VAL Chi-restraints excluded: chain H residue 645 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 22 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 171 optimal weight: 0.8980 chunk 0 optimal weight: 70.0000 chunk 268 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 185 optimal weight: 20.0000 chunk 143 optimal weight: 4.9990 chunk 285 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 383 ASN E 383 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.161600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.107458 restraints weight = 45897.387| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.18 r_work: 0.2990 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 33659 Z= 0.223 Angle : 0.641 12.807 45418 Z= 0.307 Chirality : 0.041 0.170 5299 Planarity : 0.004 0.045 5862 Dihedral : 4.537 17.100 4710 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 2.86 % Allowed : 17.97 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 4212 helix: 0.30 (0.10), residues: 2942 sheet: -1.77 (0.36), residues: 152 loop : -2.03 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 162 TYR 0.011 0.002 TYR B 687 PHE 0.016 0.001 PHE C 617 TRP 0.004 0.001 TRP B 412 HIS 0.004 0.001 HIS E 236 Details of bonding type rmsd covalent geometry : bond 0.00542 (33659) covalent geometry : angle 0.64141 (45418) hydrogen bonds : bond 0.04361 ( 1722) hydrogen bonds : angle 3.57256 ( 5022) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 238 time to evaluate : 1.189 Fit side-chains REVERT: A 147 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6469 (mm) REVERT: A 489 ASP cc_start: 0.8781 (m-30) cc_final: 0.8571 (m-30) REVERT: B 330 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8741 (mp) REVERT: B 399 GLU cc_start: 0.8183 (mp0) cc_final: 0.7392 (tt0) REVERT: C 147 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6349 (mm) REVERT: D 143 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6708 (tt0) REVERT: D 147 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6438 (mm) REVERT: D 330 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8749 (mp) REVERT: E 147 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6417 (mm) REVERT: E 489 ASP cc_start: 0.8773 (m-30) cc_final: 0.8565 (m-30) REVERT: F 147 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6246 (mm) REVERT: F 217 ARG cc_start: 0.8229 (mmt90) cc_final: 0.7666 (mmm-85) REVERT: F 330 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8737 (mp) REVERT: F 399 GLU cc_start: 0.7151 (tt0) cc_final: 0.6646 (tt0) REVERT: G 147 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6347 (mm) REVERT: G 489 ASP cc_start: 0.8773 (m-30) cc_final: 0.8554 (m-30) REVERT: H 330 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8747 (mp) REVERT: H 399 GLU cc_start: 0.7297 (tt0) cc_final: 0.6787 (tt0) outliers start: 96 outliers final: 46 residues processed: 307 average time/residue: 0.2064 time to fit residues: 103.8110 Evaluate side-chains 288 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 231 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 383 ASN Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 383 ASN Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 539 LEU Chi-restraints excluded: chain E residue 593 ILE Chi-restraints excluded: chain E residue 618 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 173 LYS Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain G residue 618 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 618 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 68 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 291 optimal weight: 0.1980 chunk 147 optimal weight: 4.9990 chunk 275 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 366 optimal weight: 0.8980 chunk 384 optimal weight: 7.9990 chunk 301 optimal weight: 1.9990 chunk 293 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 383 ASN H 156 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.164441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109506 restraints weight = 46001.551| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.86 r_work: 0.3083 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33659 Z= 0.112 Angle : 0.579 12.706 45418 Z= 0.272 Chirality : 0.038 0.164 5299 Planarity : 0.003 0.043 5862 Dihedral : 4.242 17.333 4710 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.59 % Allowed : 18.77 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.13), residues: 4212 helix: 0.64 (0.10), residues: 2926 sheet: -1.36 (0.39), residues: 152 loop : -1.92 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 543 TYR 0.008 0.001 TYR E 380 PHE 0.014 0.001 PHE G 617 TRP 0.004 0.001 TRP C 490 HIS 0.002 0.000 HIS G 236 Details of bonding type rmsd covalent geometry : bond 0.00262 (33659) covalent geometry : angle 0.57901 (45418) hydrogen bonds : bond 0.03188 ( 1722) hydrogen bonds : angle 3.36997 ( 5022) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 241 time to evaluate : 1.197 Fit side-chains REVERT: A 147 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6423 (mm) REVERT: A 514 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8967 (mt) REVERT: B 330 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8686 (mp) REVERT: B 399 GLU cc_start: 0.8227 (mp0) cc_final: 0.7366 (tt0) REVERT: B 489 ASP cc_start: 0.8897 (m-30) cc_final: 0.8339 (m-30) REVERT: C 147 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6296 (mm) REVERT: D 143 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6729 (tt0) REVERT: D 147 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6352 (mm) REVERT: D 330 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8709 (mp) REVERT: D 489 ASP cc_start: 0.8906 (m-30) cc_final: 0.8332 (m-30) REVERT: E 147 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6427 (mm) REVERT: E 248 LYS cc_start: 0.8309 (mttt) cc_final: 0.8089 (mtmt) REVERT: E 489 ASP cc_start: 0.8890 (m-30) cc_final: 0.8681 (m-30) REVERT: F 147 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6239 (mm) REVERT: F 217 ARG cc_start: 0.8258 (mmt90) cc_final: 0.7773 (mmm-85) REVERT: F 330 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8716 (mp) REVERT: F 399 GLU cc_start: 0.7037 (tt0) cc_final: 0.6510 (tt0) REVERT: F 489 ASP cc_start: 0.8865 (m-30) cc_final: 0.8302 (m-30) REVERT: G 147 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6507 (mm) REVERT: G 489 ASP cc_start: 0.8883 (m-30) cc_final: 0.8664 (m-30) REVERT: H 330 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8752 (mp) REVERT: H 399 GLU cc_start: 0.7241 (tt0) cc_final: 0.6676 (tt0) REVERT: H 489 ASP cc_start: 0.8885 (m-30) cc_final: 0.8326 (m-30) outliers start: 87 outliers final: 49 residues processed: 301 average time/residue: 0.2040 time to fit residues: 99.9348 Evaluate side-chains 296 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 235 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 593 ILE Chi-restraints excluded: chain E residue 618 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain G residue 593 ILE Chi-restraints excluded: chain G residue 618 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 618 VAL Chi-restraints excluded: chain H residue 645 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 82 optimal weight: 1.9990 chunk 201 optimal weight: 7.9990 chunk 338 optimal weight: 3.9990 chunk 329 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 182 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 336 optimal weight: 0.9980 chunk 403 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.163726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108785 restraints weight = 45727.834| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.82 r_work: 0.3077 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 33659 Z= 0.131 Angle : 0.591 12.695 45418 Z= 0.276 Chirality : 0.038 0.160 5299 Planarity : 0.004 0.040 5862 Dihedral : 4.218 15.735 4710 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.68 % Allowed : 19.24 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.13), residues: 4212 helix: 0.78 (0.10), residues: 2910 sheet: -1.17 (0.40), residues: 152 loop : -1.94 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 392 TYR 0.008 0.001 TYR B 687 PHE 0.017 0.001 PHE C 617 TRP 0.005 0.001 TRP A 490 HIS 0.002 0.000 HIS G 236 Details of bonding type rmsd covalent geometry : bond 0.00313 (33659) covalent geometry : angle 0.59149 (45418) hydrogen bonds : bond 0.03451 ( 1722) hydrogen bonds : angle 3.34060 ( 5022) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 237 time to evaluate : 1.163 Fit side-chains REVERT: A 147 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6402 (mm) REVERT: A 514 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8983 (mt) REVERT: B 330 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8747 (mp) REVERT: B 399 GLU cc_start: 0.8200 (mp0) cc_final: 0.7319 (tt0) REVERT: B 489 ASP cc_start: 0.8896 (m-30) cc_final: 0.8358 (m-30) REVERT: C 147 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6547 (mm) REVERT: D 143 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6769 (tt0) REVERT: D 147 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6374 (mm) REVERT: D 330 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8728 (mp) REVERT: D 489 ASP cc_start: 0.8915 (m-30) cc_final: 0.8350 (m-30) REVERT: E 147 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6538 (mm) REVERT: F 147 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6396 (mm) REVERT: F 217 ARG cc_start: 0.8270 (mmt90) cc_final: 0.7726 (mmm-85) REVERT: F 330 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8710 (mp) REVERT: F 489 ASP cc_start: 0.8869 (m-30) cc_final: 0.8323 (m-30) REVERT: G 147 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6550 (mm) REVERT: G 489 ASP cc_start: 0.8895 (m-30) cc_final: 0.8686 (m-30) REVERT: H 330 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8735 (mp) REVERT: H 399 GLU cc_start: 0.7215 (tt0) cc_final: 0.6648 (tt0) REVERT: H 489 ASP cc_start: 0.8898 (m-30) cc_final: 0.8446 (m-30) outliers start: 90 outliers final: 56 residues processed: 303 average time/residue: 0.1940 time to fit residues: 97.1532 Evaluate side-chains 303 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 235 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 383 ASN Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 593 ILE Chi-restraints excluded: chain E residue 618 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 621 LEU Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain G residue 593 ILE Chi-restraints excluded: chain G residue 618 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 618 VAL Chi-restraints excluded: chain H residue 621 LEU Chi-restraints excluded: chain H residue 645 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 41 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 30.0000 chunk 240 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 223 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 385 optimal weight: 10.0000 chunk 224 optimal weight: 8.9990 chunk 401 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.164795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110860 restraints weight = 45749.538| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.86 r_work: 0.3059 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33659 Z= 0.114 Angle : 0.584 13.223 45418 Z= 0.269 Chirality : 0.038 0.158 5299 Planarity : 0.004 0.053 5862 Dihedral : 4.097 16.740 4710 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.41 % Allowed : 19.66 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.13), residues: 4212 helix: 0.90 (0.10), residues: 2934 sheet: -0.88 (0.41), residues: 152 loop : -1.89 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 392 TYR 0.007 0.001 TYR D 687 PHE 0.017 0.001 PHE C 617 TRP 0.008 0.001 TRP E 490 HIS 0.002 0.001 HIS F 236 Details of bonding type rmsd covalent geometry : bond 0.00271 (33659) covalent geometry : angle 0.58404 (45418) hydrogen bonds : bond 0.03165 ( 1722) hydrogen bonds : angle 3.29124 ( 5022) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 247 time to evaluate : 1.172 Fit side-chains REVERT: A 147 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6372 (mm) REVERT: A 514 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8930 (mt) REVERT: B 330 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8665 (mp) REVERT: B 399 GLU cc_start: 0.8120 (mp0) cc_final: 0.7254 (tt0) REVERT: B 489 ASP cc_start: 0.8888 (m-30) cc_final: 0.8319 (m-30) REVERT: C 147 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6397 (mm) REVERT: D 143 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6676 (tt0) REVERT: D 147 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6272 (mm) REVERT: D 330 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8661 (mp) REVERT: D 489 ASP cc_start: 0.8905 (m-30) cc_final: 0.8336 (m-30) REVERT: E 147 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6440 (mm) REVERT: E 248 LYS cc_start: 0.8186 (mttt) cc_final: 0.7971 (mtpt) REVERT: F 147 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6264 (mm) REVERT: F 217 ARG cc_start: 0.8239 (mmt90) cc_final: 0.7651 (mmm-85) REVERT: F 330 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8652 (mp) REVERT: F 489 ASP cc_start: 0.8873 (m-30) cc_final: 0.8312 (m-30) REVERT: G 147 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6454 (mm) REVERT: G 489 ASP cc_start: 0.8876 (m-30) cc_final: 0.8667 (m-30) REVERT: H 162 ARG cc_start: 0.7795 (mmm160) cc_final: 0.7525 (mmm-85) REVERT: H 330 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8680 (mp) REVERT: H 399 GLU cc_start: 0.7156 (tt0) cc_final: 0.6561 (tt0) REVERT: H 489 ASP cc_start: 0.8871 (m-30) cc_final: 0.8307 (m-30) outliers start: 81 outliers final: 57 residues processed: 301 average time/residue: 0.2095 time to fit residues: 102.4020 Evaluate side-chains 312 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 243 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 383 ASN Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 593 ILE Chi-restraints excluded: chain E residue 618 VAL Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 656 ILE Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 621 LEU Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain G residue 593 ILE Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 621 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 25 optimal weight: 1.9990 chunk 399 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 191 optimal weight: 0.9990 chunk 258 optimal weight: 6.9990 chunk 93 optimal weight: 0.0980 chunk 82 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 640 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.166794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.112894 restraints weight = 46002.680| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.90 r_work: 0.3093 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33659 Z= 0.093 Angle : 0.569 12.733 45418 Z= 0.261 Chirality : 0.037 0.156 5299 Planarity : 0.004 0.055 5862 Dihedral : 3.874 14.472 4710 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.75 % Allowed : 20.40 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 4212 helix: 1.13 (0.10), residues: 2942 sheet: -0.47 (0.43), residues: 152 loop : -1.90 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 392 TYR 0.005 0.001 TYR B 687 PHE 0.022 0.001 PHE A 617 TRP 0.006 0.001 TRP G 214 HIS 0.002 0.000 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00208 (33659) covalent geometry : angle 0.56882 (45418) hydrogen bonds : bond 0.02737 ( 1722) hydrogen bonds : angle 3.17152 ( 5022) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 265 time to evaluate : 0.987 Fit side-chains REVERT: A 395 ARG cc_start: 0.7695 (ttm110) cc_final: 0.7309 (mtt90) REVERT: B 330 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8644 (mp) REVERT: B 392 ARG cc_start: 0.8596 (ttt90) cc_final: 0.8336 (ttt90) REVERT: B 399 GLU cc_start: 0.8100 (mp0) cc_final: 0.7215 (tt0) REVERT: B 489 ASP cc_start: 0.8883 (m-30) cc_final: 0.8364 (m-30) REVERT: C 147 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6045 (mm) REVERT: C 395 ARG cc_start: 0.7690 (ttm110) cc_final: 0.7304 (mtt90) REVERT: D 143 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6654 (tt0) REVERT: D 147 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6287 (mm) REVERT: D 489 ASP cc_start: 0.8892 (m-30) cc_final: 0.8441 (m-30) REVERT: E 147 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6024 (mm) REVERT: E 395 ARG cc_start: 0.7689 (ttm110) cc_final: 0.7255 (mtt90) REVERT: F 147 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6214 (mm) REVERT: F 217 ARG cc_start: 0.8219 (mmt90) cc_final: 0.7681 (mmm-85) REVERT: F 392 ARG cc_start: 0.8604 (ttt90) cc_final: 0.8334 (ttt90) REVERT: F 489 ASP cc_start: 0.8854 (m-30) cc_final: 0.8420 (m-30) REVERT: G 147 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6168 (mm) REVERT: H 162 ARG cc_start: 0.7774 (mmm160) cc_final: 0.7538 (mmm-85) REVERT: H 392 ARG cc_start: 0.8559 (ttt90) cc_final: 0.8270 (ttt90) REVERT: H 399 GLU cc_start: 0.7069 (tt0) cc_final: 0.6485 (tt0) REVERT: H 489 ASP cc_start: 0.8887 (m-30) cc_final: 0.8374 (m-30) outliers start: 59 outliers final: 36 residues processed: 307 average time/residue: 0.2105 time to fit residues: 103.4044 Evaluate side-chains 290 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 593 ILE Chi-restraints excluded: chain E residue 618 VAL Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 263 ASP Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 593 ILE Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 515 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 293 optimal weight: 3.9990 chunk 24 optimal weight: 0.0870 chunk 258 optimal weight: 3.9990 chunk 222 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 426 optimal weight: 20.0000 chunk 427 optimal weight: 8.9990 chunk 320 optimal weight: 20.0000 chunk 172 optimal weight: 4.9990 chunk 285 optimal weight: 9.9990 chunk 392 optimal weight: 2.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 383 ASN C 516 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.162796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.108190 restraints weight = 45693.715| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.28 r_work: 0.2961 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 33659 Z= 0.185 Angle : 0.638 13.272 45418 Z= 0.296 Chirality : 0.040 0.159 5299 Planarity : 0.004 0.058 5862 Dihedral : 4.250 15.629 4710 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.78 % Allowed : 20.61 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.13), residues: 4212 helix: 0.95 (0.10), residues: 2918 sheet: -0.56 (0.43), residues: 152 loop : -1.90 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 543 TYR 0.009 0.001 TYR H 687 PHE 0.025 0.001 PHE A 617 TRP 0.005 0.001 TRP A 638 HIS 0.004 0.001 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00451 (33659) covalent geometry : angle 0.63831 (45418) hydrogen bonds : bond 0.03945 ( 1722) hydrogen bonds : angle 3.36697 ( 5022) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9023.27 seconds wall clock time: 154 minutes 22.59 seconds (9262.59 seconds total)