Starting phenix.real_space_refine on Thu Mar 5 23:23:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v4j_21041/03_2026/6v4j_21041_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v4j_21041/03_2026/6v4j_21041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6v4j_21041/03_2026/6v4j_21041_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v4j_21041/03_2026/6v4j_21041_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v4j_21041/03_2026/6v4j_21041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v4j_21041/03_2026/6v4j_21041.map" } resolution = 2.97 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7018 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 13526 2.51 5 N 3346 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s 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: 20637 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3450 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 17, 'TRANS': 429} Chain breaks: 5 Chain: "B" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3354 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 16, 'TRANS': 417} Chain breaks: 6 Chain: "C" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3414 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 424} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3390 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 17, 'TRANS': 420} Chain breaks: 5 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1748 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 227} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1767 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 2 Chain: "G" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1753 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1761 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.79, per 1000 atoms: 0.23 Number of scatterers: 20637 At special positions: 0 Unit cell: (120.474, 177.606, 109.296, 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 105 16.00 O 3660 8.00 N 3346 7.00 C 13526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 348 " distance=2.05 Simple disulfide: pdb=" SG CYS B 251 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 251 " - pdb=" SG CYS C 348 " distance=1.59 Simple disulfide: pdb=" SG CYS D 251 " - pdb=" SG CYS D 348 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 1.0 seconds 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4974 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 8 sheets defined 62.8% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 2 through 20 removed outlier: 3.772A pdb=" N ILE A 6 " --> pdb=" O GLN A 2 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG A 8 " --> pdb=" O ARG A 4 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 22 No H-bonds generated for 'chain 'A' and resid 21 through 22' Processing helix chain 'A' and resid 23 through 27 removed outlier: 3.727A pdb=" N LEU A 26 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 48 removed outlier: 3.781A pdb=" N LEU A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.739A pdb=" N LEU A 89 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 124 through 149 removed outlier: 3.731A pdb=" N MET A 140 " --> pdb=" O TRP A 136 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 202 removed outlier: 4.517A pdb=" N ALA A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TRP A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 235 through 252 removed outlier: 3.968A pdb=" N CYS A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 removed outlier: 4.114A pdb=" N ALA A 258 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 273 through 298 removed outlier: 4.063A pdb=" N ARG A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 319 Processing helix chain 'A' and resid 333 through 345 removed outlier: 4.560A pdb=" N VAL A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 377 Processing helix chain 'A' and resid 392 through 420 removed outlier: 4.133A pdb=" N VAL A 396 " --> pdb=" O PRO A 392 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 442 through 446 removed outlier: 4.107A pdb=" N ALA A 446 " --> pdb=" O GLY A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 Processing helix chain 'A' and resid 471 through 479 removed outlier: 4.152A pdb=" N LEU A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 20 removed outlier: 3.594A pdb=" N ILE B 6 " --> pdb=" O GLN B 2 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR B 20 " --> pdb=" O LEU B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 22 No H-bonds generated for 'chain 'B' and resid 21 through 22' Processing helix chain 'B' and resid 23 through 27 removed outlier: 3.575A pdb=" N LEU B 26 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 55 Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 78 through 82 removed outlier: 4.099A pdb=" N GLY B 81 " --> pdb=" O THR B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.688A pdb=" N LEU B 89 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 124 through 149 removed outlier: 3.652A pdb=" N ILE B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 203 removed outlier: 4.495A pdb=" N ALA B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 235 through 251 removed outlier: 3.598A pdb=" N ALA B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N CYS B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 removed outlier: 4.083A pdb=" N ALA B 258 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 298 Processing helix chain 'B' and resid 302 through 319 removed outlier: 3.520A pdb=" N ALA B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.731A pdb=" N ILE B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 392 through 420 removed outlier: 4.105A pdb=" N VAL B 396 " --> pdb=" O PRO B 392 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP B 397 " --> pdb=" O GLN B 393 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 437 Processing helix chain 'B' and resid 453 through 469 Processing helix chain 'B' and resid 471 through 479 removed outlier: 3.651A pdb=" N LEU B 475 " --> pdb=" O ILE B 471 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 20 removed outlier: 3.738A pdb=" N ILE C 6 " --> pdb=" O GLN C 2 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG C 8 " --> pdb=" O ARG C 4 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.722A pdb=" N LEU C 26 " --> pdb=" O ALA C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 53 Processing helix chain 'C' and resid 69 through 80 removed outlier: 3.818A pdb=" N LEU C 80 " --> pdb=" O PHE C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.720A pdb=" N LEU C 89 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 111 removed outlier: 3.896A pdb=" N THR C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 145 removed outlier: 3.732A pdb=" N ILE C 143 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 203 removed outlier: 4.409A pdb=" N ALA C 184 " --> pdb=" O GLU C 180 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TRP C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 235 through 251 removed outlier: 4.070A pdb=" N CYS C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 258 removed outlier: 4.147A pdb=" N ALA C 258 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 268 through 273 Processing helix chain 'C' and resid 273 through 298 removed outlier: 3.941A pdb=" N ARG C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 319 removed outlier: 3.724A pdb=" N ALA C 306 " --> pdb=" O SER C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 345 removed outlier: 3.710A pdb=" N ILE C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 375 removed outlier: 3.584A pdb=" N LEU C 375 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 420 removed outlier: 4.163A pdb=" N VAL C 396 " --> pdb=" O PRO C 392 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP C 397 " --> pdb=" O GLN C 393 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA C 398 " --> pdb=" O ARG C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 437 Processing helix chain 'C' and resid 453 through 469 Processing helix chain 'C' and resid 470 through 473 Processing helix chain 'C' and resid 474 through 479 removed outlier: 4.277A pdb=" N LEU C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 474 through 479' Processing helix chain 'D' and resid 2 through 20 removed outlier: 3.727A pdb=" N ILE D 6 " --> pdb=" O GLN D 2 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG D 8 " --> pdb=" O ARG D 4 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 removed outlier: 3.673A pdb=" N LEU D 26 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 55 Processing helix chain 'D' and resid 69 through 82 Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.682A pdb=" N PHE D 88 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 89 " --> pdb=" O LEU D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 89' Processing helix chain 'D' and resid 97 through 109 Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 124 through 143 removed outlier: 3.713A pdb=" N ILE D 143 " --> pdb=" O GLY D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 202 removed outlier: 4.493A pdb=" N ALA D 184 " --> pdb=" O GLU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 217 Processing helix chain 'D' and resid 235 through 251 removed outlier: 3.600A pdb=" N ALA D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 261 removed outlier: 4.034A pdb=" N ALA D 258 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 3.585A pdb=" N TYR D 270 " --> pdb=" O PRO D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 298 Processing helix chain 'D' and resid 302 through 319 removed outlier: 3.561A pdb=" N ALA D 306 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 345 removed outlier: 3.731A pdb=" N ILE D 345 " --> pdb=" O PHE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 377 Processing helix chain 'D' and resid 392 through 420 removed outlier: 4.110A pdb=" N VAL D 396 " --> pdb=" O PRO D 392 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP D 397 " --> pdb=" O GLN D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.572A pdb=" N ALA D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 469 Processing helix chain 'D' and resid 471 through 479 removed outlier: 4.201A pdb=" N LEU D 475 " --> pdb=" O ILE D 471 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 477 " --> pdb=" O THR D 473 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 54 through 61 Processing helix chain 'E' and resid 75 through 91 Processing helix chain 'E' and resid 101 through 106 Processing helix chain 'E' and resid 107 through 112 Processing helix chain 'E' and resid 241 through 252 Processing helix chain 'E' and resid 264 through 271 removed outlier: 3.906A pdb=" N LYS E 269 " --> pdb=" O GLN E 265 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU E 270 " --> pdb=" O ARG E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 291 removed outlier: 3.879A pdb=" N LEU E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 298 removed outlier: 3.668A pdb=" N VAL E 298 " --> pdb=" O ILE E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 322 removed outlier: 3.833A pdb=" N ASN E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 334 No H-bonds generated for 'chain 'E' and resid 332 through 334' Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 350 through 355 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'F' and resid 9 through 20 Processing helix chain 'F' and resid 54 through 61 Processing helix chain 'F' and resid 75 through 91 Processing helix chain 'F' and resid 101 through 106 Processing helix chain 'F' and resid 107 through 112 Processing helix chain 'F' and resid 243 through 252 Processing helix chain 'F' and resid 264 through 274 Processing helix chain 'F' and resid 286 through 291 removed outlier: 4.286A pdb=" N LEU F 290 " --> pdb=" O ASP F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 298 removed outlier: 3.711A pdb=" N VAL F 298 " --> pdb=" O ILE F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 321 Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 349 through 360 removed outlier: 4.359A pdb=" N ALA F 353 " --> pdb=" O SER F 349 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR F 354 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 20 Processing helix chain 'G' and resid 54 through 61 Processing helix chain 'G' and resid 75 through 91 Processing helix chain 'G' and resid 101 through 106 Processing helix chain 'G' and resid 107 through 112 Processing helix chain 'G' and resid 241 through 252 Processing helix chain 'G' and resid 264 through 274 Processing helix chain 'G' and resid 286 through 291 removed outlier: 4.307A pdb=" N LEU G 290 " --> pdb=" O ASP G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 298 removed outlier: 3.722A pdb=" N VAL G 298 " --> pdb=" O ILE G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 321 Processing helix chain 'G' and resid 335 through 340 Processing helix chain 'G' and resid 350 through 355 Processing helix chain 'G' and resid 355 through 360 Processing helix chain 'H' and resid 9 through 20 Processing helix chain 'H' and resid 54 through 61 Processing helix chain 'H' and resid 75 through 91 Processing helix chain 'H' and resid 101 through 106 Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'H' and resid 243 through 252 Processing helix chain 'H' and resid 264 through 274 Processing helix chain 'H' and resid 286 through 291 removed outlier: 4.277A pdb=" N LEU H 290 " --> pdb=" O ASP H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 298 removed outlier: 3.746A pdb=" N VAL H 298 " --> pdb=" O ILE H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 309 through 321 Processing helix chain 'H' and resid 335 through 340 Processing helix chain 'H' and resid 350 through 355 Processing helix chain 'H' and resid 355 through 360 Processing sheet with id=AA1, first strand: chain 'E' and resid 48 through 49 removed outlier: 8.139A pdb=" N VAL E 48 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE E 28 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 278 through 281 removed outlier: 6.382A pdb=" N PHE E 301 " --> pdb=" O MET E 327 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU E 329 " --> pdb=" O PHE E 301 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ALA E 303 " --> pdb=" O LEU E 329 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ILE E 348 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL E 328 " --> pdb=" O ILE E 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 48 through 49 removed outlier: 8.139A pdb=" N VAL F 48 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE F 28 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 278 through 281 removed outlier: 5.933A pdb=" N VAL F 257 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N PHE F 280 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU F 259 " --> pdb=" O PHE F 280 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE F 301 " --> pdb=" O MET F 327 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU F 329 " --> pdb=" O PHE F 301 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA F 303 " --> pdb=" O LEU F 329 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL F 326 " --> pdb=" O VAL F 346 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE F 348 " --> pdb=" O VAL F 326 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL F 328 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 48 through 49 removed outlier: 8.139A pdb=" N VAL G 48 " --> pdb=" O ILE G 26 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE G 28 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 278 through 281 removed outlier: 5.966A pdb=" N VAL G 257 " --> pdb=" O ILE G 278 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE G 280 " --> pdb=" O VAL G 257 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU G 259 " --> pdb=" O PHE G 280 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE G 348 " --> pdb=" O VAL G 326 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL G 328 " --> pdb=" O ILE G 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 48 through 49 removed outlier: 8.139A pdb=" N VAL H 48 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE H 28 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS H 2 " --> pdb=" O MET H 68 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL H 70 " --> pdb=" O LYS H 2 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE H 4 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU H 69 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 278 through 281 removed outlier: 5.826A pdb=" N VAL H 257 " --> pdb=" O ILE H 278 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N PHE H 280 " --> pdb=" O VAL H 257 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU H 259 " --> pdb=" O PHE H 280 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE H 348 " --> pdb=" O VAL H 326 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL H 328 " --> pdb=" O ILE H 348 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3270 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: 3.75 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.71 - 0.94: 1 0.94 - 1.17: 1 1.17 - 1.40: 8552 1.40 - 1.63: 12350 1.63 - 1.86: 174 Bond restraints: 21078 Sorted by residual: bond pdb=" C LEU E 69 " pdb=" N VAL E 70 " ideal model delta sigma weight residual 1.332 0.705 0.627 1.23e-02 6.61e+03 2.60e+03 bond pdb=" C MET E 68 " pdb=" N LEU E 69 " ideal model delta sigma weight residual 1.329 1.567 -0.238 1.40e-02 5.10e+03 2.88e+02 bond pdb=" C ASN E 18 " pdb=" N LEU E 19 " ideal model delta sigma weight residual 1.333 1.130 0.203 1.43e-02 4.89e+03 2.02e+02 bond pdb=" C LEU E 19 " pdb=" N VAL E 20 " ideal model delta sigma weight residual 1.332 1.488 -0.156 1.36e-02 5.41e+03 1.31e+02 bond pdb=" CA SER F 314 " pdb=" C SER F 314 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.29e-02 6.01e+03 1.09e+01 ... (remaining 21073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.24: 28519 9.24 - 18.49: 123 18.49 - 27.73: 5 27.73 - 36.97: 1 36.97 - 46.21: 3 Bond angle restraints: 28651 Sorted by residual: angle pdb=" O MET E 68 " pdb=" C MET E 68 " pdb=" N LEU E 69 " ideal model delta sigma weight residual 123.25 77.04 46.21 1.14e+00 7.69e-01 1.64e+03 angle pdb=" CA MET E 68 " pdb=" C MET E 68 " pdb=" N LEU E 69 " ideal model delta sigma weight residual 115.36 161.19 -45.83 1.48e+00 4.57e-01 9.59e+02 angle pdb=" C MET E 68 " pdb=" N LEU E 69 " pdb=" CA LEU E 69 " ideal model delta sigma weight residual 121.70 162.96 -41.26 1.80e+00 3.09e-01 5.25e+02 angle pdb=" C ASN E 18 " pdb=" N LEU E 19 " pdb=" CA LEU E 19 " ideal model delta sigma weight residual 121.92 86.82 35.10 1.73e+00 3.34e-01 4.12e+02 angle pdb=" CA ASN E 18 " pdb=" C ASN E 18 " pdb=" N LEU E 19 " ideal model delta sigma weight residual 118.17 96.79 21.38 1.33e+00 5.65e-01 2.58e+02 ... (remaining 28646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 11046 16.74 - 33.48: 951 33.48 - 50.22: 165 50.22 - 66.96: 32 66.96 - 83.69: 18 Dihedral angle restraints: 12212 sinusoidal: 4518 harmonic: 7694 Sorted by residual: dihedral pdb=" CA CYS C 251 " pdb=" C CYS C 251 " pdb=" N ASN C 252 " pdb=" CA ASN C 252 " ideal model delta harmonic sigma weight residual 180.00 -96.39 -83.61 0 5.00e+00 4.00e-02 2.80e+02 dihedral pdb=" CA GLU B 275 " pdb=" C GLU B 275 " pdb=" N PHE B 276 " pdb=" CA PHE B 276 " ideal model delta harmonic sigma weight residual 180.00 -130.51 -49.49 0 5.00e+00 4.00e-02 9.80e+01 dihedral pdb=" CA VAL C 118 " pdb=" C VAL C 118 " pdb=" N GLY C 119 " pdb=" CA GLY C 119 " ideal model delta harmonic sigma weight residual -180.00 -139.24 -40.76 0 5.00e+00 4.00e-02 6.65e+01 ... (remaining 12209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2930 0.123 - 0.246: 424 0.246 - 0.369: 70 0.369 - 0.492: 11 0.492 - 0.615: 6 Chirality restraints: 3441 Sorted by residual: chirality pdb=" CB VAL D 445 " pdb=" CA VAL D 445 " pdb=" CG1 VAL D 445 " pdb=" CG2 VAL D 445 " both_signs ideal model delta sigma weight residual False -2.63 -2.01 -0.62 2.00e-01 2.50e+01 9.47e+00 chirality pdb=" CB ILE B 220 " pdb=" CA ILE B 220 " pdb=" CG1 ILE B 220 " pdb=" CG2 ILE B 220 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.68e+00 chirality pdb=" CA ASP H 308 " pdb=" N ASP H 308 " pdb=" C ASP H 308 " pdb=" CB ASP H 308 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.90e+00 ... (remaining 3438 not shown) Planarity restraints: 3553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 55 " -0.102 5.00e-02 4.00e+02 1.49e-01 3.53e+01 pdb=" N PRO B 56 " 0.257 5.00e-02 4.00e+02 pdb=" CA PRO B 56 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO B 56 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 19 " -0.035 2.00e-02 2.50e+03 5.89e-02 3.47e+01 pdb=" C LEU E 19 " 0.102 2.00e-02 2.50e+03 pdb=" O LEU E 19 " -0.034 2.00e-02 2.50e+03 pdb=" N VAL E 20 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 466 " -0.026 2.00e-02 2.50e+03 5.15e-02 2.66e+01 pdb=" C PHE C 466 " 0.089 2.00e-02 2.50e+03 pdb=" O PHE C 466 " -0.033 2.00e-02 2.50e+03 pdb=" N GLY C 467 " -0.030 2.00e-02 2.50e+03 ... (remaining 3550 not shown) Histogram of nonbonded interaction distances: 0.24 - 1.18: 11 1.18 - 2.11: 78 2.11 - 3.04: 12770 3.04 - 3.97: 52828 3.97 - 4.90: 91129 Warning: very small nonbonded interaction distances. Nonbonded interactions: 156816 Sorted by model distance: nonbonded pdb=" CD GLU F 77 " pdb=" CD GLU H 77 " model vdw 0.244 3.500 nonbonded pdb=" SD MET F 68 " pdb=" CG LEU F 358 " model vdw 1.061 3.830 nonbonded pdb=" OE2 GLU F 107 " pdb=" CE1 HIS H 54 " model vdw 1.082 3.260 nonbonded pdb=" CE1 HIS F 54 " pdb=" OE2 GLU H 107 " model vdw 1.090 3.260 nonbonded pdb=" OD1 ASP G 308 " pdb=" NE2 GLN G 331 " model vdw 1.096 3.120 ... (remaining 156811 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 1 through 28 or resid 37 through 89 or resid 94 through 11 \ 7 or resid 124 through 153 or resid 178 through 267 or (resid 268 and (name N or \ name CA or name C or name O or name CB )) or resid 269 through 270 or resid 275 \ through 483)) selection = (chain 'B' and (resid 1 through 28 or resid 37 through 61 or resid 68 through 11 \ 7 or resid 124 through 267 or (resid 268 and (name N or name CA or name C or nam \ e O or name CB )) or resid 269 through 483)) selection = (chain 'C' and (resid 1 through 28 or resid 37 through 89 or resid 94 through 11 \ 7 or resid 124 through 270 or resid 275 through 483)) selection = (chain 'D' and (resid 1 through 28 or resid 37 through 89 or resid 94 through 11 \ 7 or resid 124 through 267 or (resid 268 and (name N or name CA or name C or nam \ e O or name CB )) or resid 269 through 270 or resid 275 through 483)) } ncs_group { reference = (chain 'E' and (resid 1 through 308 or (resid 309 and (name N or name CA or name \ C or name O or name CB )) or resid 310 through 360)) selection = (chain 'F' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 67 or (resid 68 and (name N or name \ CA or name C or name O or name CB )) or resid 69 through 76 or (resid 77 and (n \ ame N or name CA or name C or name O or name CB )) or resid 78 through 308 or (r \ esid 309 and (name N or name CA or name C or name O or name CB )) or resid 310 t \ hrough 331 or (resid 332 and (name N or name CA or name C or name O or name CB ) \ ) or resid 333 through 357 or (resid 358 and (name N or name CA or name C or nam \ e O or name CB )) or resid 359 through 360)) selection = (chain 'G' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 331 or (resid 332 and (name N or na \ me CA or name C or name O or name CB )) or resid 333 through 360)) selection = (chain 'H' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 76 or (resid 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 308 or (resid 309 and \ (name N or name CA or name C or name O or name CB )) or resid 310 through 331 or \ (resid 332 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 3 through 360)) } 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.510 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4896 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 : 0.011 0.627 21082 Z= 0.623 Angle : 1.805 46.214 28659 Z= 1.035 Chirality : 0.094 0.615 3441 Planarity : 0.011 0.149 3553 Dihedral : 13.199 83.694 7226 Min Nonbonded Distance : 0.244 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.00 % Favored : 95.65 % Rotamer: Outliers : 5.36 % Allowed : 10.55 % Favored : 84.09 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.54 (0.15), residues: 2623 helix: 0.95 (0.13), residues: 1393 sheet: -0.70 (0.41), residues: 180 loop : -2.17 (0.16), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 370 TYR 0.029 0.003 TYR A 304 PHE 0.070 0.005 PHE B 323 TRP 0.064 0.005 TRP B 400 HIS 0.022 0.003 HIS D 448 Details of bonding type rmsd covalent geometry : bond 0.01037 (21078) covalent geometry : angle 1.78996 (28651) SS BOND : bond 0.22262 ( 4) SS BOND : angle 14.21539 ( 8) hydrogen bonds : bond 0.17348 ( 1128) hydrogen bonds : angle 9.23122 ( 3270) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 596 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.6290 (ttp80) cc_final: 0.5987 (ttp-170) REVERT: A 21 MET cc_start: 0.6115 (mmt) cc_final: 0.5888 (mmm) REVERT: A 79 VAL cc_start: 0.5977 (OUTLIER) cc_final: 0.5691 (t) REVERT: A 143 ILE cc_start: 0.6518 (pt) cc_final: 0.6315 (tt) REVERT: A 200 PHE cc_start: 0.6002 (m-10) cc_final: 0.5529 (m-80) REVERT: A 270 TYR cc_start: 0.7170 (m-10) cc_final: 0.6822 (m-80) REVERT: A 280 ILE cc_start: 0.7403 (mm) cc_final: 0.7195 (mp) REVERT: A 293 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6733 (tm) REVERT: A 311 LEU cc_start: 0.6454 (tm) cc_final: 0.6162 (mm) REVERT: A 331 TRP cc_start: 0.7039 (m100) cc_final: 0.6690 (m100) REVERT: A 339 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7531 (mp) REVERT: A 343 SER cc_start: 0.7404 (p) cc_final: 0.6988 (m) REVERT: A 345 ILE cc_start: 0.6880 (mt) cc_final: 0.6631 (tp) REVERT: A 356 MET cc_start: 0.7967 (ptp) cc_final: 0.7734 (ptm) REVERT: A 359 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.7083 (tt) REVERT: A 370 ARG cc_start: 0.6663 (ttt180) cc_final: 0.6281 (mmt-90) REVERT: A 385 LYS cc_start: 0.7044 (ptpt) cc_final: 0.6387 (ptmm) REVERT: A 447 LEU cc_start: 0.5868 (OUTLIER) cc_final: 0.5405 (mm) REVERT: A 460 LEU cc_start: 0.7262 (mt) cc_final: 0.7001 (mm) REVERT: A 470 GLU cc_start: 0.5591 (OUTLIER) cc_final: 0.5127 (tp30) REVERT: A 477 LEU cc_start: 0.7581 (mm) cc_final: 0.7159 (mt) REVERT: B 21 MET cc_start: 0.6383 (mmt) cc_final: 0.6139 (mmm) REVERT: B 60 HIS cc_start: 0.5192 (t70) cc_final: 0.4927 (t70) REVERT: B 103 PHE cc_start: 0.6899 (t80) cc_final: 0.6698 (t80) REVERT: B 104 GLU cc_start: 0.7428 (tp30) cc_final: 0.6985 (tp30) REVERT: B 153 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7037 (pp) REVERT: B 188 ILE cc_start: 0.7159 (mm) cc_final: 0.6864 (pt) REVERT: B 190 LEU cc_start: 0.7141 (tm) cc_final: 0.6758 (tp) REVERT: B 201 TRP cc_start: 0.6640 (t60) cc_final: 0.6092 (t60) REVERT: B 207 PRO cc_start: 0.7307 (Cg_exo) cc_final: 0.7089 (Cg_endo) REVERT: B 211 ILE cc_start: 0.6398 (mt) cc_final: 0.6114 (pp) REVERT: B 236 TYR cc_start: 0.7403 (m-80) cc_final: 0.7052 (m-80) REVERT: B 311 LEU cc_start: 0.6419 (tm) cc_final: 0.6150 (mm) REVERT: B 334 PHE cc_start: 0.6288 (t80) cc_final: 0.5677 (t80) REVERT: B 339 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7385 (mp) REVERT: B 343 SER cc_start: 0.6826 (p) cc_final: 0.6491 (m) REVERT: B 370 ARG cc_start: 0.6297 (ttt180) cc_final: 0.5895 (mmm160) REVERT: B 373 LYS cc_start: 0.7100 (mtpp) cc_final: 0.6275 (mtpp) REVERT: B 382 TYR cc_start: 0.5072 (m-80) cc_final: 0.4239 (m-80) REVERT: B 391 LEU cc_start: 0.7644 (pp) cc_final: 0.7089 (tp) REVERT: B 397 ASP cc_start: 0.7028 (m-30) cc_final: 0.6770 (m-30) REVERT: B 466 PHE cc_start: 0.6429 (m-10) cc_final: 0.6217 (m-80) REVERT: B 477 LEU cc_start: 0.6686 (mm) cc_final: 0.6383 (mp) REVERT: C 70 PHE cc_start: 0.6342 (m-80) cc_final: 0.6128 (m-10) REVERT: C 74 VAL cc_start: 0.6467 (t) cc_final: 0.6261 (m) REVERT: C 130 TYR cc_start: 0.5788 (t80) cc_final: 0.5568 (t80) REVERT: C 143 ILE cc_start: 0.7303 (pt) cc_final: 0.6601 (tp) REVERT: C 190 LEU cc_start: 0.6906 (tm) cc_final: 0.6577 (tp) REVERT: C 270 TYR cc_start: 0.7021 (m-10) cc_final: 0.6774 (m-80) REVERT: C 292 LEU cc_start: 0.6946 (mt) cc_final: 0.6739 (mt) REVERT: C 311 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.6115 (mm) REVERT: C 331 TRP cc_start: 0.6906 (m100) cc_final: 0.6222 (m-90) REVERT: C 339 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7573 (mp) REVERT: C 345 ILE cc_start: 0.6641 (mt) cc_final: 0.6416 (tp) REVERT: C 356 MET cc_start: 0.7676 (ptp) cc_final: 0.7267 (ptm) REVERT: C 373 LYS cc_start: 0.7328 (mtpp) cc_final: 0.6757 (mtpp) REVERT: C 382 TYR cc_start: 0.5061 (m-80) cc_final: 0.4572 (m-80) REVERT: C 385 LYS cc_start: 0.6865 (ptpt) cc_final: 0.6401 (pttm) REVERT: C 392 PRO cc_start: 0.7508 (Cg_endo) cc_final: 0.7180 (Cg_exo) REVERT: D 8 ARG cc_start: 0.6643 (ttp80) cc_final: 0.6321 (ttp-170) REVERT: D 21 MET cc_start: 0.6238 (mmt) cc_final: 0.5549 (mmm) REVERT: D 189 TYR cc_start: 0.6875 (OUTLIER) cc_final: 0.6423 (t80) REVERT: D 190 LEU cc_start: 0.7159 (tm) cc_final: 0.6776 (tp) REVERT: D 280 ILE cc_start: 0.7718 (mm) cc_final: 0.7471 (mp) REVERT: D 311 LEU cc_start: 0.6245 (tm) cc_final: 0.5933 (mm) REVERT: D 312 PHE cc_start: 0.6016 (t80) cc_final: 0.5777 (t80) REVERT: D 331 TRP cc_start: 0.6739 (m100) cc_final: 0.6136 (m-90) REVERT: D 339 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7594 (mp) REVERT: D 356 MET cc_start: 0.8125 (ptp) cc_final: 0.7685 (ptm) REVERT: D 358 VAL cc_start: 0.7102 (t) cc_final: 0.6656 (p) REVERT: D 359 ILE cc_start: 0.7535 (pp) cc_final: 0.7139 (pt) REVERT: D 361 ILE cc_start: 0.6497 (mm) cc_final: 0.6195 (tt) REVERT: D 362 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6227 (mp) REVERT: D 370 ARG cc_start: 0.6501 (ttt180) cc_final: 0.5373 (ptt180) REVERT: D 373 LYS cc_start: 0.7381 (mtpp) cc_final: 0.6646 (mtpp) REVERT: D 382 TYR cc_start: 0.5187 (m-80) cc_final: 0.4228 (m-80) REVERT: D 385 LYS cc_start: 0.6786 (ptpt) cc_final: 0.6506 (ptmm) REVERT: D 423 ASP cc_start: 0.6563 (p0) cc_final: 0.6303 (p0) REVERT: D 476 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7676 (pt) REVERT: D 477 LEU cc_start: 0.7270 (mm) cc_final: 0.6982 (tp) REVERT: E 242 ASN cc_start: 0.7148 (m110) cc_final: 0.6896 (m-40) REVERT: E 259 LEU cc_start: 0.5080 (tt) cc_final: 0.4752 (tm) REVERT: E 260 ILE cc_start: 0.6103 (mt) cc_final: 0.5471 (mm) REVERT: E 293 GLU cc_start: 0.5473 (OUTLIER) cc_final: 0.5139 (mp0) REVERT: E 301 PHE cc_start: 0.6468 (t80) cc_final: 0.6205 (t80) REVERT: E 308 ASP cc_start: 0.3976 (OUTLIER) cc_final: 0.3696 (p0) REVERT: E 309 GLU cc_start: 0.4449 (OUTLIER) cc_final: 0.3639 (pm20) REVERT: F 1 MET cc_start: -0.0126 (tpp) cc_final: -0.0349 (mmm) REVERT: F 259 LEU cc_start: 0.5293 (tt) cc_final: 0.4854 (tm) REVERT: F 260 ILE cc_start: 0.6101 (mt) cc_final: 0.5437 (mm) REVERT: F 294 ASN cc_start: 0.6897 (m-40) cc_final: 0.6580 (m-40) REVERT: F 309 GLU cc_start: 0.3230 (OUTLIER) cc_final: 0.2980 (pp20) REVERT: F 325 LYS cc_start: 0.6021 (tttt) cc_final: 0.5425 (mppt) REVERT: F 328 VAL cc_start: 0.6916 (t) cc_final: 0.6562 (p) REVERT: F 348 ILE cc_start: 0.6957 (mp) cc_final: 0.6602 (pt) REVERT: G 238 VAL cc_start: 0.6418 (m) cc_final: 0.6178 (p) REVERT: G 259 LEU cc_start: 0.5536 (tt) cc_final: 0.5215 (tm) REVERT: G 275 GLU cc_start: 0.4800 (tp30) cc_final: 0.4371 (tp30) REVERT: G 294 ASN cc_start: 0.6772 (m-40) cc_final: 0.6505 (m-40) REVERT: G 313 MET cc_start: 0.5254 (mmm) cc_final: 0.4947 (mmm) REVERT: H 246 SER cc_start: 0.7747 (t) cc_final: 0.7290 (m) REVERT: H 279 VAL cc_start: 0.4304 (OUTLIER) cc_final: 0.3720 (p) REVERT: H 294 ASN cc_start: 0.6848 (m-40) cc_final: 0.6550 (m-40) REVERT: H 313 MET cc_start: 0.5283 (mmm) cc_final: 0.4975 (mmm) outliers start: 117 outliers final: 40 residues processed: 691 average time/residue: 0.3632 time to fit residues: 306.1838 Evaluate side-chains 485 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 426 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 305 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 436 ASN A 448 HIS A 453 ASN B 57 ASN B 60 HIS ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS B 266 HIS ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 HIS ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 HIS C 377 HIS C 453 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 HIS D 377 HIS D 448 HIS F 311 ASN G 91 ASN G 121 HIS H 91 ASN H 311 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.240028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.230551 restraints weight = 33009.456| |-----------------------------------------------------------------------------| r_work (start): 0.4704 rms_B_bonded: 0.79 r_work: 0.4616 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.4553 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.4553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5157 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21082 Z= 0.156 Angle : 0.775 16.184 28659 Z= 0.384 Chirality : 0.046 0.349 3441 Planarity : 0.005 0.081 3553 Dihedral : 8.004 105.880 2907 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.67 % Favored : 97.29 % Rotamer: Outliers : 5.23 % Allowed : 16.00 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 (0.15), residues: 2623 helix: 0.13 (0.13), residues: 1400 sheet: -0.35 (0.37), residues: 200 loop : -1.79 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 360 TYR 0.020 0.002 TYR E 104 PHE 0.028 0.002 PHE B 291 TRP 0.025 0.002 TRP D 400 HIS 0.004 0.001 HIS D 448 Details of bonding type rmsd covalent geometry : bond 0.00305 (21078) covalent geometry : angle 0.77492 (28651) SS BOND : bond 0.00702 ( 4) SS BOND : angle 1.85746 ( 8) hydrogen bonds : bond 0.05802 ( 1128) hydrogen bonds : angle 6.26201 ( 3270) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 484 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.6742 (ttp80) cc_final: 0.6524 (ttp80) REVERT: A 21 MET cc_start: 0.6473 (mmt) cc_final: 0.6025 (mmm) REVERT: A 45 VAL cc_start: 0.6107 (p) cc_final: 0.5698 (m) REVERT: A 104 GLU cc_start: 0.6999 (tp30) cc_final: 0.6755 (tp30) REVERT: A 143 ILE cc_start: 0.7288 (pt) cc_final: 0.6941 (tp) REVERT: A 155 ILE cc_start: 0.3177 (pt) cc_final: 0.2305 (mp) REVERT: A 343 SER cc_start: 0.6749 (p) cc_final: 0.6396 (p) REVERT: A 385 LYS cc_start: 0.6786 (ptpt) cc_final: 0.6475 (ptmm) REVERT: A 391 LEU cc_start: 0.7338 (mt) cc_final: 0.7133 (mm) REVERT: A 447 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5741 (mm) REVERT: A 470 GLU cc_start: 0.6114 (OUTLIER) cc_final: 0.5797 (tp30) REVERT: A 477 LEU cc_start: 0.7290 (mm) cc_final: 0.7001 (mt) REVERT: B 54 TRP cc_start: 0.7015 (t-100) cc_final: 0.6801 (t-100) REVERT: B 188 ILE cc_start: 0.7318 (mm) cc_final: 0.7103 (pt) REVERT: B 190 LEU cc_start: 0.7178 (tm) cc_final: 0.6795 (tp) REVERT: B 201 TRP cc_start: 0.6680 (t60) cc_final: 0.6328 (t60) REVERT: B 238 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6729 (mm) REVERT: B 277 ARG cc_start: 0.5000 (ptp90) cc_final: 0.4270 (ptt-90) REVERT: B 382 TYR cc_start: 0.3304 (m-80) cc_final: 0.2997 (m-80) REVERT: B 423 ASP cc_start: 0.6499 (p0) cc_final: 0.6231 (p0) REVERT: C 54 TRP cc_start: 0.7186 (t-100) cc_final: 0.6916 (t-100) REVERT: C 190 LEU cc_start: 0.7131 (tm) cc_final: 0.6778 (tp) REVERT: C 238 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7063 (mm) REVERT: C 256 HIS cc_start: 0.7214 (m-70) cc_final: 0.6980 (m-70) REVERT: C 271 TRP cc_start: 0.7479 (t-100) cc_final: 0.7020 (t-100) REVERT: C 356 MET cc_start: 0.7786 (ptp) cc_final: 0.7331 (ptm) REVERT: C 382 TYR cc_start: 0.4049 (m-80) cc_final: 0.3809 (m-80) REVERT: C 392 PRO cc_start: 0.7404 (Cg_endo) cc_final: 0.6980 (Cg_exo) REVERT: C 395 VAL cc_start: 0.7838 (t) cc_final: 0.7558 (m) REVERT: D 8 ARG cc_start: 0.6821 (ttp80) cc_final: 0.6495 (ttp-110) REVERT: D 21 MET cc_start: 0.6428 (mmt) cc_final: 0.5943 (mmm) REVERT: D 54 TRP cc_start: 0.7110 (t-100) cc_final: 0.6854 (t-100) REVERT: D 102 PHE cc_start: 0.6344 (m-80) cc_final: 0.6137 (m-80) REVERT: D 104 GLU cc_start: 0.7254 (tp30) cc_final: 0.6977 (tp30) REVERT: D 107 SER cc_start: 0.5348 (OUTLIER) cc_final: 0.5138 (p) REVERT: D 190 LEU cc_start: 0.7104 (tm) cc_final: 0.6725 (tp) REVERT: D 202 LEU cc_start: 0.5874 (OUTLIER) cc_final: 0.5547 (tp) REVERT: D 382 TYR cc_start: 0.3582 (m-80) cc_final: 0.3122 (m-80) REVERT: D 423 ASP cc_start: 0.6725 (p0) cc_final: 0.6473 (p0) REVERT: E 236 MET cc_start: 0.4028 (mtp) cc_final: 0.3739 (tpp) REVERT: E 326 VAL cc_start: 0.7691 (m) cc_final: 0.7334 (t) REVERT: F 68 MET cc_start: 0.2383 (ttm) cc_final: 0.1931 (mmm) REVERT: F 238 VAL cc_start: 0.6176 (OUTLIER) cc_final: 0.5796 (p) REVERT: F 358 LEU cc_start: 0.1668 (OUTLIER) cc_final: 0.1448 (tp) REVERT: G 236 MET cc_start: 0.3397 (mtp) cc_final: 0.3151 (tpp) REVERT: G 238 VAL cc_start: 0.6508 (m) cc_final: 0.6290 (p) REVERT: G 327 MET cc_start: 0.7028 (OUTLIER) cc_final: 0.6450 (tmt) REVERT: H 246 SER cc_start: 0.7241 (t) cc_final: 0.7020 (m) outliers start: 114 outliers final: 40 residues processed: 563 average time/residue: 0.4054 time to fit residues: 274.2205 Evaluate side-chains 435 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 386 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 305 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 77 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 232 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 202 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 437 ASN B 57 ASN B 213 HIS B 367 GLN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 HIS ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 453 ASN D 213 HIS ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN E 91 ASN E 311 ASN F 91 ASN G 18 ASN H 91 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.233543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.226401 restraints weight = 32065.937| |-----------------------------------------------------------------------------| r_work (start): 0.4663 rms_B_bonded: 0.55 r_work: 0.4577 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.4515 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.4515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5287 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 21082 Z= 0.227 Angle : 0.773 16.275 28659 Z= 0.395 Chirality : 0.047 0.338 3441 Planarity : 0.005 0.073 3553 Dihedral : 6.767 57.494 2840 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 6.83 % Allowed : 15.86 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.84 (0.15), residues: 2623 helix: -0.67 (0.13), residues: 1372 sheet: -0.00 (0.42), residues: 152 loop : -2.04 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 360 TYR 0.032 0.002 TYR B 304 PHE 0.026 0.002 PHE B 334 TRP 0.029 0.002 TRP B 400 HIS 0.004 0.001 HIS B 377 Details of bonding type rmsd covalent geometry : bond 0.00429 (21078) covalent geometry : angle 0.77309 (28651) SS BOND : bond 0.00185 ( 4) SS BOND : angle 0.96300 ( 8) hydrogen bonds : bond 0.06377 ( 1128) hydrogen bonds : angle 6.62209 ( 3270) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 433 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.6530 (mmt) cc_final: 0.5903 (mmm) REVERT: A 103 PHE cc_start: 0.6519 (t80) cc_final: 0.6289 (t80) REVERT: A 132 GLN cc_start: 0.7204 (mm-40) cc_final: 0.6999 (mm110) REVERT: A 143 ILE cc_start: 0.7161 (pt) cc_final: 0.6673 (tp) REVERT: A 343 SER cc_start: 0.6955 (p) cc_final: 0.6389 (m) REVERT: A 344 PHE cc_start: 0.7102 (m-80) cc_final: 0.6858 (m-80) REVERT: A 382 TYR cc_start: 0.4112 (m-80) cc_final: 0.3264 (m-80) REVERT: A 385 LYS cc_start: 0.6857 (ptpt) cc_final: 0.6500 (pttm) REVERT: A 391 LEU cc_start: 0.7451 (mt) cc_final: 0.7243 (mp) REVERT: A 423 ASP cc_start: 0.6751 (p0) cc_final: 0.6505 (p0) REVERT: A 447 LEU cc_start: 0.6316 (OUTLIER) cc_final: 0.6024 (mm) REVERT: A 470 GLU cc_start: 0.5767 (OUTLIER) cc_final: 0.5083 (mm-30) REVERT: A 477 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6962 (mt) REVERT: B 21 MET cc_start: 0.6461 (mmt) cc_final: 0.5985 (mmm) REVERT: B 54 TRP cc_start: 0.7119 (t-100) cc_final: 0.6914 (t-100) REVERT: B 188 ILE cc_start: 0.7367 (mm) cc_final: 0.7136 (pt) REVERT: B 190 LEU cc_start: 0.7103 (tm) cc_final: 0.6788 (tp) REVERT: B 201 TRP cc_start: 0.6850 (t60) cc_final: 0.6434 (t60) REVERT: B 238 ILE cc_start: 0.7036 (OUTLIER) cc_final: 0.6691 (mm) REVERT: B 277 ARG cc_start: 0.5283 (ptp90) cc_final: 0.4045 (ttt-90) REVERT: B 334 PHE cc_start: 0.5640 (t80) cc_final: 0.5285 (t80) REVERT: B 382 TYR cc_start: 0.4384 (m-80) cc_final: 0.3289 (m-80) REVERT: B 466 PHE cc_start: 0.6321 (m-10) cc_final: 0.6109 (m-10) REVERT: C 103 PHE cc_start: 0.6758 (t80) cc_final: 0.6515 (t80) REVERT: C 190 LEU cc_start: 0.7091 (tm) cc_final: 0.6749 (tp) REVERT: C 201 TRP cc_start: 0.6923 (t60) cc_final: 0.6589 (t60) REVERT: C 238 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.6925 (mm) REVERT: C 373 LYS cc_start: 0.6061 (mtpp) cc_final: 0.5668 (mtpp) REVERT: C 382 TYR cc_start: 0.4845 (m-80) cc_final: 0.2603 (m-80) REVERT: D 8 ARG cc_start: 0.6737 (ttp80) cc_final: 0.6529 (ttp80) REVERT: D 21 MET cc_start: 0.6537 (mmt) cc_final: 0.6116 (mmm) REVERT: D 60 HIS cc_start: 0.7050 (t-90) cc_final: 0.6528 (t-90) REVERT: D 102 PHE cc_start: 0.6261 (m-80) cc_final: 0.6021 (m-80) REVERT: D 103 PHE cc_start: 0.6635 (t80) cc_final: 0.6334 (t80) REVERT: D 190 LEU cc_start: 0.7040 (tm) cc_final: 0.6683 (tp) REVERT: D 202 LEU cc_start: 0.6316 (OUTLIER) cc_final: 0.5758 (tp) REVERT: D 238 ILE cc_start: 0.7494 (tt) cc_final: 0.7122 (mm) REVERT: D 345 ILE cc_start: 0.7780 (tp) cc_final: 0.7555 (tt) REVERT: D 366 LEU cc_start: 0.6656 (mp) cc_final: 0.6424 (mt) REVERT: D 373 LYS cc_start: 0.6318 (OUTLIER) cc_final: 0.6013 (tttt) REVERT: D 382 TYR cc_start: 0.4611 (m-80) cc_final: 0.3375 (m-80) REVERT: E 327 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6681 (mpp) REVERT: F 68 MET cc_start: 0.2396 (ttm) cc_final: 0.1652 (mpp) REVERT: F 238 VAL cc_start: 0.6308 (OUTLIER) cc_final: 0.5975 (p) REVERT: F 349 SER cc_start: 0.6724 (t) cc_final: 0.6458 (p) REVERT: G 238 VAL cc_start: 0.6637 (m) cc_final: 0.6359 (p) REVERT: G 327 MET cc_start: 0.6842 (OUTLIER) cc_final: 0.6361 (mpp) outliers start: 149 outliers final: 65 residues processed: 534 average time/residue: 0.4167 time to fit residues: 265.3528 Evaluate side-chains 465 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 390 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 236 MET Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 305 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 107 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 0.2980 chunk 232 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 216 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 313 GLN B 213 HIS B 313 GLN C 213 HIS C 313 GLN D 213 HIS D 313 GLN E 91 ASN F 18 ASN G 253 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.234561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.224296 restraints weight = 32289.385| |-----------------------------------------------------------------------------| r_work (start): 0.4654 rms_B_bonded: 0.93 r_work: 0.4561 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.4499 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.4499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5265 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21082 Z= 0.144 Angle : 0.676 13.925 28659 Z= 0.338 Chirality : 0.043 0.294 3441 Planarity : 0.005 0.073 3553 Dihedral : 6.033 59.574 2829 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.64 % Allowed : 19.39 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.62 (0.15), residues: 2623 helix: -0.50 (0.13), residues: 1395 sheet: -0.00 (0.41), residues: 152 loop : -1.94 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 370 TYR 0.026 0.001 TYR B 304 PHE 0.021 0.001 PHE B 334 TRP 0.017 0.001 TRP B 331 HIS 0.004 0.001 HIS C 448 Details of bonding type rmsd covalent geometry : bond 0.00281 (21078) covalent geometry : angle 0.67558 (28651) SS BOND : bond 0.00482 ( 4) SS BOND : angle 1.15285 ( 8) hydrogen bonds : bond 0.05043 ( 1128) hydrogen bonds : angle 6.06082 ( 3270) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 421 time to evaluate : 0.724 Fit side-chains REVERT: A 8 ARG cc_start: 0.6517 (ttp80) cc_final: 0.6202 (ttp-110) REVERT: A 21 MET cc_start: 0.6508 (mmt) cc_final: 0.5846 (mmm) REVERT: A 103 PHE cc_start: 0.6554 (t80) cc_final: 0.6308 (t80) REVERT: A 143 ILE cc_start: 0.7184 (pt) cc_final: 0.6626 (tp) REVERT: A 343 SER cc_start: 0.6780 (p) cc_final: 0.6197 (m) REVERT: A 361 ILE cc_start: 0.5670 (mt) cc_final: 0.5390 (tt) REVERT: A 382 TYR cc_start: 0.3972 (m-80) cc_final: 0.3113 (m-80) REVERT: A 385 LYS cc_start: 0.6844 (ptpt) cc_final: 0.6518 (ptmm) REVERT: A 423 ASP cc_start: 0.6963 (p0) cc_final: 0.6517 (p0) REVERT: A 447 LEU cc_start: 0.6338 (OUTLIER) cc_final: 0.5670 (mm) REVERT: A 477 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7082 (mt) REVERT: A 478 LEU cc_start: 0.7153 (tp) cc_final: 0.6914 (mt) REVERT: B 21 MET cc_start: 0.6563 (mmt) cc_final: 0.6143 (mmm) REVERT: B 54 TRP cc_start: 0.7113 (t-100) cc_final: 0.6868 (t-100) REVERT: B 103 PHE cc_start: 0.6715 (t80) cc_final: 0.6454 (t80) REVERT: B 190 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6711 (tp) REVERT: B 201 TRP cc_start: 0.6758 (t60) cc_final: 0.6274 (t60) REVERT: B 205 MET cc_start: 0.4338 (ptp) cc_final: 0.4082 (ptp) REVERT: B 277 ARG cc_start: 0.5291 (ptp90) cc_final: 0.4181 (ttt-90) REVERT: B 382 TYR cc_start: 0.4637 (m-80) cc_final: 0.3039 (m-80) REVERT: C 21 MET cc_start: 0.6715 (mmm) cc_final: 0.6202 (mmm) REVERT: C 54 TRP cc_start: 0.7297 (t-100) cc_final: 0.7046 (t-100) REVERT: C 103 PHE cc_start: 0.6668 (t80) cc_final: 0.6444 (t80) REVERT: C 190 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6763 (tp) REVERT: C 201 TRP cc_start: 0.6614 (t60) cc_final: 0.6162 (t60) REVERT: C 238 ILE cc_start: 0.7113 (OUTLIER) cc_final: 0.6751 (mm) REVERT: C 356 MET cc_start: 0.7437 (ptm) cc_final: 0.7079 (ptm) REVERT: C 373 LYS cc_start: 0.6216 (mtpp) cc_final: 0.5653 (mtpp) REVERT: C 382 TYR cc_start: 0.4495 (m-80) cc_final: 0.3925 (m-80) REVERT: C 469 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6356 (pt) REVERT: D 8 ARG cc_start: 0.6834 (ttp80) cc_final: 0.6498 (ttp80) REVERT: D 21 MET cc_start: 0.6605 (mmt) cc_final: 0.6246 (mmm) REVERT: D 60 HIS cc_start: 0.6849 (t-90) cc_final: 0.6387 (t-90) REVERT: D 102 PHE cc_start: 0.6380 (m-80) cc_final: 0.6167 (m-80) REVERT: D 103 PHE cc_start: 0.6625 (t80) cc_final: 0.6293 (t80) REVERT: D 104 GLU cc_start: 0.7323 (tp30) cc_final: 0.7121 (tp30) REVERT: D 190 LEU cc_start: 0.7090 (tm) cc_final: 0.6727 (tp) REVERT: D 202 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5609 (tp) REVERT: D 238 ILE cc_start: 0.7258 (tt) cc_final: 0.6814 (mm) REVERT: D 345 ILE cc_start: 0.7508 (tp) cc_final: 0.7252 (tt) REVERT: D 373 LYS cc_start: 0.6409 (OUTLIER) cc_final: 0.6159 (tttt) REVERT: D 382 TYR cc_start: 0.4130 (m-80) cc_final: 0.3169 (m-80) REVERT: D 423 ASP cc_start: 0.6754 (p0) cc_final: 0.6494 (p0) REVERT: E 236 MET cc_start: 0.4210 (OUTLIER) cc_final: 0.3881 (tpp) REVERT: E 327 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6487 (mpp) REVERT: F 68 MET cc_start: 0.2163 (ttm) cc_final: 0.1490 (mpt) REVERT: F 238 VAL cc_start: 0.6241 (OUTLIER) cc_final: 0.5886 (p) REVERT: F 349 SER cc_start: 0.6897 (t) cc_final: 0.6585 (p) REVERT: G 236 MET cc_start: 0.3464 (OUTLIER) cc_final: 0.3248 (tpp) REVERT: G 238 VAL cc_start: 0.6493 (m) cc_final: 0.6203 (p) REVERT: G 327 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6470 (mpp) REVERT: H 275 GLU cc_start: 0.4917 (tp30) cc_final: 0.3963 (tt0) outliers start: 123 outliers final: 52 residues processed: 492 average time/residue: 0.4352 time to fit residues: 254.3352 Evaluate side-chains 454 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 389 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 236 MET Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 305 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 37 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 222 optimal weight: 0.0970 chunk 65 optimal weight: 0.7980 chunk 34 optimal weight: 0.0070 chunk 116 optimal weight: 6.9990 chunk 232 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 HIS C 213 HIS C 313 GLN D 213 HIS D 313 GLN E 91 ASN F 91 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.237812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.230785 restraints weight = 31756.476| |-----------------------------------------------------------------------------| r_work (start): 0.4711 rms_B_bonded: 0.56 r_work: 0.4632 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.4567 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.4567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5138 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21082 Z= 0.121 Angle : 0.642 12.056 28659 Z= 0.317 Chirality : 0.042 0.251 3441 Planarity : 0.004 0.068 3553 Dihedral : 5.550 59.289 2824 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.50 % Allowed : 20.54 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.24 (0.15), residues: 2623 helix: -0.14 (0.13), residues: 1386 sheet: 0.30 (0.41), residues: 152 loop : -1.86 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 370 TYR 0.031 0.001 TYR B 304 PHE 0.021 0.001 PHE C 312 TRP 0.016 0.001 TRP D 331 HIS 0.004 0.001 HIS C 448 Details of bonding type rmsd covalent geometry : bond 0.00242 (21078) covalent geometry : angle 0.64234 (28651) SS BOND : bond 0.00405 ( 4) SS BOND : angle 0.91843 ( 8) hydrogen bonds : bond 0.04430 ( 1128) hydrogen bonds : angle 5.63816 ( 3270) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 419 time to evaluate : 0.722 Fit side-chains REVERT: A 21 MET cc_start: 0.6463 (mmt) cc_final: 0.5903 (mmm) REVERT: A 47 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6305 (mm) REVERT: A 103 PHE cc_start: 0.6434 (t80) cc_final: 0.6180 (t80) REVERT: A 143 ILE cc_start: 0.6905 (pt) cc_final: 0.6445 (tp) REVERT: A 271 TRP cc_start: 0.7298 (t-100) cc_final: 0.6967 (t-100) REVERT: A 361 ILE cc_start: 0.5854 (mt) cc_final: 0.5549 (tt) REVERT: A 373 LYS cc_start: 0.5619 (OUTLIER) cc_final: 0.5336 (tttt) REVERT: A 382 TYR cc_start: 0.3486 (m-80) cc_final: 0.3119 (m-80) REVERT: A 385 LYS cc_start: 0.6621 (ptpt) cc_final: 0.6278 (mtmm) REVERT: A 469 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6117 (mm) REVERT: A 477 LEU cc_start: 0.7355 (mm) cc_final: 0.7148 (mt) REVERT: B 6 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6876 (mt) REVERT: B 21 MET cc_start: 0.6500 (mmt) cc_final: 0.6180 (mmm) REVERT: B 103 PHE cc_start: 0.6628 (t80) cc_final: 0.6374 (t80) REVERT: B 201 TRP cc_start: 0.6795 (t60) cc_final: 0.6469 (t60) REVERT: B 205 MET cc_start: 0.4423 (ptp) cc_final: 0.4034 (ptp) REVERT: B 277 ARG cc_start: 0.5104 (ptp90) cc_final: 0.4055 (mtm-85) REVERT: B 376 VAL cc_start: 0.6850 (t) cc_final: 0.6556 (t) REVERT: B 377 HIS cc_start: 0.7056 (OUTLIER) cc_final: 0.6775 (m-70) REVERT: B 382 TYR cc_start: 0.3244 (m-80) cc_final: 0.2061 (m-80) REVERT: B 423 ASP cc_start: 0.6967 (p0) cc_final: 0.6703 (p0) REVERT: C 103 PHE cc_start: 0.6578 (t80) cc_final: 0.6342 (t80) REVERT: C 120 LEU cc_start: 0.6089 (OUTLIER) cc_final: 0.5708 (tt) REVERT: C 190 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6445 (tp) REVERT: C 201 TRP cc_start: 0.6552 (t60) cc_final: 0.6147 (t60) REVERT: C 356 MET cc_start: 0.7521 (ptm) cc_final: 0.7176 (ptm) REVERT: C 373 LYS cc_start: 0.5781 (mtpp) cc_final: 0.5290 (mtpp) REVERT: C 382 TYR cc_start: 0.4082 (m-80) cc_final: 0.3730 (m-80) REVERT: C 423 ASP cc_start: 0.6590 (p0) cc_final: 0.6370 (p0) REVERT: C 469 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6257 (pt) REVERT: D 8 ARG cc_start: 0.6735 (ttp80) cc_final: 0.6524 (ttp80) REVERT: D 21 MET cc_start: 0.6487 (mmt) cc_final: 0.6099 (mmm) REVERT: D 60 HIS cc_start: 0.6883 (t-90) cc_final: 0.6404 (t-90) REVERT: D 102 PHE cc_start: 0.6464 (m-80) cc_final: 0.6210 (m-80) REVERT: D 103 PHE cc_start: 0.6567 (t80) cc_final: 0.6228 (t80) REVERT: D 190 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6524 (tp) REVERT: D 201 TRP cc_start: 0.6550 (t60) cc_final: 0.6159 (t60) REVERT: D 202 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5653 (tp) REVERT: D 423 ASP cc_start: 0.6615 (p0) cc_final: 0.6368 (p0) REVERT: E 236 MET cc_start: 0.4108 (OUTLIER) cc_final: 0.3846 (tpp) REVERT: E 327 MET cc_start: 0.6746 (OUTLIER) cc_final: 0.6355 (mpp) REVERT: F 238 VAL cc_start: 0.5864 (OUTLIER) cc_final: 0.5614 (p) REVERT: G 327 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6364 (mpp) REVERT: G 328 VAL cc_start: 0.7256 (p) cc_final: 0.7039 (t) REVERT: H 275 GLU cc_start: 0.4947 (tp30) cc_final: 0.4624 (tt0) REVERT: H 301 PHE cc_start: 0.6271 (t80) cc_final: 0.5866 (t80) outliers start: 120 outliers final: 52 residues processed: 490 average time/residue: 0.4192 time to fit residues: 243.7959 Evaluate side-chains 444 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 378 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 189 TYR Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 189 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 326 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 104 optimal weight: 0.8980 chunk 190 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 259 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN A 448 HIS B 213 HIS ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 HIS C 213 HIS C 313 GLN D 213 HIS D 313 GLN E 91 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.234624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.227521 restraints weight = 31585.358| |-----------------------------------------------------------------------------| r_work (start): 0.4675 rms_B_bonded: 0.54 r_work: 0.4599 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.4545 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.4545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5207 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21082 Z= 0.165 Angle : 0.719 16.547 28659 Z= 0.353 Chirality : 0.044 0.242 3441 Planarity : 0.005 0.070 3553 Dihedral : 5.632 57.651 2820 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 5.32 % Allowed : 22.38 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.49 (0.15), residues: 2623 helix: -0.41 (0.13), residues: 1380 sheet: 0.50 (0.42), residues: 152 loop : -1.92 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 379 TYR 0.027 0.001 TYR B 304 PHE 0.022 0.002 PHE B 291 TRP 0.017 0.002 TRP B 331 HIS 0.004 0.001 HIS C 448 Details of bonding type rmsd covalent geometry : bond 0.00319 (21078) covalent geometry : angle 0.71855 (28651) SS BOND : bond 0.00234 ( 4) SS BOND : angle 0.56285 ( 8) hydrogen bonds : bond 0.05176 ( 1128) hydrogen bonds : angle 5.99300 ( 3270) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 402 time to evaluate : 0.761 Fit side-chains REVERT: A 21 MET cc_start: 0.6633 (mmt) cc_final: 0.6114 (mmm) REVERT: A 47 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6316 (mm) REVERT: A 103 PHE cc_start: 0.6420 (t80) cc_final: 0.6180 (t80) REVERT: A 143 ILE cc_start: 0.6986 (pt) cc_final: 0.6518 (tp) REVERT: A 201 TRP cc_start: 0.6218 (t60) cc_final: 0.5932 (t60) REVERT: A 271 TRP cc_start: 0.7259 (t-100) cc_final: 0.6960 (t-100) REVERT: A 361 ILE cc_start: 0.5532 (mt) cc_final: 0.5270 (tt) REVERT: A 382 TYR cc_start: 0.3852 (m-80) cc_final: 0.3211 (m-80) REVERT: A 385 LYS cc_start: 0.6643 (ptpt) cc_final: 0.6394 (mtmm) REVERT: A 477 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7041 (mt) REVERT: B 21 MET cc_start: 0.6534 (mmt) cc_final: 0.6313 (mmm) REVERT: B 103 PHE cc_start: 0.6636 (t80) cc_final: 0.6368 (t80) REVERT: B 131 ARG cc_start: 0.6676 (ptp-170) cc_final: 0.6462 (ptm160) REVERT: B 201 TRP cc_start: 0.6752 (t60) cc_final: 0.6523 (t60) REVERT: B 277 ARG cc_start: 0.5338 (OUTLIER) cc_final: 0.3940 (mtm-85) REVERT: B 382 TYR cc_start: 0.4004 (m-80) cc_final: 0.2798 (m-80) REVERT: C 103 PHE cc_start: 0.6634 (t80) cc_final: 0.6346 (t80) REVERT: C 120 LEU cc_start: 0.6134 (OUTLIER) cc_final: 0.5739 (tt) REVERT: C 201 TRP cc_start: 0.6551 (t60) cc_final: 0.6171 (t60) REVERT: C 356 MET cc_start: 0.7496 (ptm) cc_final: 0.7157 (ptm) REVERT: C 373 LYS cc_start: 0.5808 (mtpp) cc_final: 0.5382 (mtpp) REVERT: C 382 TYR cc_start: 0.4489 (m-80) cc_final: 0.2493 (m-80) REVERT: C 469 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6292 (pt) REVERT: D 8 ARG cc_start: 0.6744 (ttp80) cc_final: 0.6538 (ttp80) REVERT: D 21 MET cc_start: 0.6537 (mmt) cc_final: 0.6101 (mmm) REVERT: D 60 HIS cc_start: 0.7083 (t-90) cc_final: 0.6595 (t-90) REVERT: D 102 PHE cc_start: 0.6377 (m-80) cc_final: 0.6147 (m-80) REVERT: D 103 PHE cc_start: 0.6503 (t80) cc_final: 0.6181 (t80) REVERT: D 190 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6453 (tp) REVERT: D 382 TYR cc_start: 0.3945 (m-80) cc_final: 0.3125 (m-80) REVERT: D 385 LYS cc_start: 0.6502 (mptp) cc_final: 0.6209 (ptmm) REVERT: D 471 ILE cc_start: 0.6370 (OUTLIER) cc_final: 0.6064 (mp) REVERT: E 236 MET cc_start: 0.4080 (OUTLIER) cc_final: 0.3875 (tpp) REVERT: E 243 ILE cc_start: 0.7193 (mt) cc_final: 0.6970 (tt) REVERT: E 260 ILE cc_start: 0.7122 (mt) cc_final: 0.6887 (mm) REVERT: F 238 VAL cc_start: 0.5930 (OUTLIER) cc_final: 0.5611 (p) REVERT: F 259 LEU cc_start: 0.6021 (tm) cc_final: 0.5816 (tp) REVERT: F 349 SER cc_start: 0.7195 (t) cc_final: 0.6951 (p) REVERT: G 246 SER cc_start: 0.7576 (t) cc_final: 0.7317 (m) REVERT: G 301 PHE cc_start: 0.6500 (t80) cc_final: 0.6114 (t80) REVERT: G 327 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6323 (mpp) REVERT: H 246 SER cc_start: 0.7478 (t) cc_final: 0.7273 (m) REVERT: H 275 GLU cc_start: 0.5174 (tp30) cc_final: 0.4452 (tt0) outliers start: 116 outliers final: 56 residues processed: 474 average time/residue: 0.4201 time to fit residues: 234.5114 Evaluate side-chains 438 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 372 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 305 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 79 optimal weight: 2.9990 chunk 199 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 240 optimal weight: 7.9990 chunk 216 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 313 GLN A 448 HIS B 213 HIS ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 HIS C 213 HIS C 313 GLN D 213 HIS D 313 GLN D 448 HIS E 91 ASN F 253 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.233344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.226159 restraints weight = 31395.796| |-----------------------------------------------------------------------------| r_work (start): 0.4659 rms_B_bonded: 0.55 r_work: 0.4583 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.4521 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5271 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21082 Z= 0.192 Angle : 0.764 17.942 28659 Z= 0.378 Chirality : 0.046 0.243 3441 Planarity : 0.005 0.066 3553 Dihedral : 5.824 56.649 2819 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.73 % Allowed : 22.60 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.81 (0.15), residues: 2623 helix: -0.70 (0.13), residues: 1381 sheet: 0.58 (0.42), residues: 152 loop : -2.07 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 8 TYR 0.030 0.002 TYR B 304 PHE 0.022 0.002 PHE B 291 TRP 0.023 0.002 TRP A 54 HIS 0.006 0.001 HIS C 448 Details of bonding type rmsd covalent geometry : bond 0.00371 (21078) covalent geometry : angle 0.76394 (28651) SS BOND : bond 0.00162 ( 4) SS BOND : angle 0.46215 ( 8) hydrogen bonds : bond 0.05614 ( 1128) hydrogen bonds : angle 6.29556 ( 3270) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 402 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.6594 (mmt) cc_final: 0.6056 (mmm) REVERT: A 47 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.6232 (mm) REVERT: A 103 PHE cc_start: 0.6421 (t80) cc_final: 0.6196 (t80) REVERT: A 143 ILE cc_start: 0.6995 (pt) cc_final: 0.6529 (tp) REVERT: A 201 TRP cc_start: 0.6292 (t60) cc_final: 0.5962 (t60) REVERT: A 361 ILE cc_start: 0.5828 (mt) cc_final: 0.5584 (tt) REVERT: A 382 TYR cc_start: 0.4300 (m-80) cc_final: 0.3098 (m-80) REVERT: A 391 LEU cc_start: 0.6683 (mm) cc_final: 0.6349 (mp) REVERT: B 8 ARG cc_start: 0.6669 (ttp-110) cc_final: 0.6307 (ttp80) REVERT: B 21 MET cc_start: 0.6498 (mmt) cc_final: 0.6271 (mmm) REVERT: B 103 PHE cc_start: 0.6646 (t80) cc_final: 0.6396 (t80) REVERT: B 201 TRP cc_start: 0.6944 (t60) cc_final: 0.6484 (t60) REVERT: B 205 MET cc_start: 0.4462 (ptp) cc_final: 0.4078 (ptp) REVERT: B 277 ARG cc_start: 0.5315 (OUTLIER) cc_final: 0.3916 (mtm-85) REVERT: B 331 TRP cc_start: 0.6680 (OUTLIER) cc_final: 0.5934 (m100) REVERT: B 382 TYR cc_start: 0.4287 (m-80) cc_final: 0.2904 (m-80) REVERT: B 423 ASP cc_start: 0.6702 (p0) cc_final: 0.6489 (p0) REVERT: C 8 ARG cc_start: 0.6348 (ttp80) cc_final: 0.6059 (ttp-170) REVERT: C 103 PHE cc_start: 0.6588 (t80) cc_final: 0.6344 (t80) REVERT: C 120 LEU cc_start: 0.6129 (OUTLIER) cc_final: 0.5867 (tt) REVERT: C 189 TYR cc_start: 0.5888 (OUTLIER) cc_final: 0.5278 (t80) REVERT: C 190 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6526 (tp) REVERT: C 201 TRP cc_start: 0.6497 (t60) cc_final: 0.6132 (t60) REVERT: C 373 LYS cc_start: 0.5985 (mtpp) cc_final: 0.5383 (mtpp) REVERT: C 382 TYR cc_start: 0.4711 (m-80) cc_final: 0.3969 (m-80) REVERT: C 469 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6458 (pt) REVERT: D 8 ARG cc_start: 0.6879 (ttp80) cc_final: 0.6624 (ttp80) REVERT: D 60 HIS cc_start: 0.7113 (t-90) cc_final: 0.6635 (t-90) REVERT: D 103 PHE cc_start: 0.6490 (t80) cc_final: 0.6257 (t80) REVERT: D 190 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6524 (tp) REVERT: D 207 PRO cc_start: 0.7663 (Cg_exo) cc_final: 0.7386 (Cg_endo) REVERT: D 238 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6798 (mm) REVERT: D 382 TYR cc_start: 0.3764 (m-80) cc_final: 0.2818 (m-80) REVERT: D 424 GLU cc_start: 0.6958 (tt0) cc_final: 0.6630 (tt0) REVERT: E 260 ILE cc_start: 0.7078 (mt) cc_final: 0.6837 (mm) REVERT: F 238 VAL cc_start: 0.5903 (OUTLIER) cc_final: 0.5586 (p) REVERT: F 259 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5885 (tp) REVERT: F 349 SER cc_start: 0.7212 (t) cc_final: 0.6978 (p) REVERT: G 327 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6372 (tmt) REVERT: H 326 VAL cc_start: 0.7809 (OUTLIER) cc_final: 0.7515 (t) REVERT: H 327 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.6491 (tmt) outliers start: 125 outliers final: 58 residues processed: 478 average time/residue: 0.4427 time to fit residues: 249.2296 Evaluate side-chains 454 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 382 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 331 TRP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 189 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 327 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 227 optimal weight: 0.0070 chunk 181 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 99 optimal weight: 0.0030 chunk 215 optimal weight: 0.0670 chunk 240 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 overall best weight: 0.3146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN A 448 HIS B 448 HIS C 213 HIS C 313 GLN D 213 HIS E 91 ASN E 311 ASN G 265 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.236872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.227266 restraints weight = 32415.040| |-----------------------------------------------------------------------------| r_work (start): 0.4689 rms_B_bonded: 0.78 r_work: 0.4620 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.4565 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.4565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5121 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21082 Z= 0.119 Angle : 0.703 16.978 28659 Z= 0.332 Chirality : 0.042 0.219 3441 Planarity : 0.004 0.069 3553 Dihedral : 5.248 56.822 2819 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.31 % Allowed : 24.39 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.17 (0.15), residues: 2623 helix: -0.14 (0.13), residues: 1387 sheet: 1.15 (0.41), residues: 156 loop : -1.90 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 8 TYR 0.031 0.001 TYR B 304 PHE 0.024 0.001 PHE B 291 TRP 0.016 0.001 TRP D 331 HIS 0.004 0.001 HIS C 448 Details of bonding type rmsd covalent geometry : bond 0.00244 (21078) covalent geometry : angle 0.70333 (28651) SS BOND : bond 0.00337 ( 4) SS BOND : angle 1.11548 ( 8) hydrogen bonds : bond 0.04192 ( 1128) hydrogen bonds : angle 5.53148 ( 3270) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 406 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 SER cc_start: 0.8289 (m) cc_final: 0.8087 (t) REVERT: A 21 MET cc_start: 0.6529 (mmt) cc_final: 0.5983 (mmm) REVERT: A 47 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6422 (mm) REVERT: A 131 ARG cc_start: 0.6599 (ptm160) cc_final: 0.6378 (ptm160) REVERT: A 143 ILE cc_start: 0.6770 (pt) cc_final: 0.6319 (tp) REVERT: A 201 TRP cc_start: 0.6181 (t60) cc_final: 0.5863 (t60) REVERT: A 294 LEU cc_start: 0.7751 (mt) cc_final: 0.7517 (mp) REVERT: A 319 THR cc_start: 0.7466 (OUTLIER) cc_final: 0.7130 (p) REVERT: A 361 ILE cc_start: 0.5521 (mt) cc_final: 0.5213 (tt) REVERT: B 103 PHE cc_start: 0.6691 (t80) cc_final: 0.6429 (t80) REVERT: B 201 TRP cc_start: 0.6771 (t60) cc_final: 0.6460 (t60) REVERT: B 277 ARG cc_start: 0.5024 (ptp90) cc_final: 0.4224 (mtm-85) REVERT: B 477 LEU cc_start: 0.7022 (mm) cc_final: 0.6754 (mt) REVERT: C 8 ARG cc_start: 0.6335 (ttp80) cc_final: 0.5977 (ttp-110) REVERT: C 12 LEU cc_start: 0.7016 (tm) cc_final: 0.6517 (pp) REVERT: C 103 PHE cc_start: 0.6553 (t80) cc_final: 0.6284 (t80) REVERT: C 120 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5704 (tt) REVERT: C 190 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6321 (tp) REVERT: C 201 TRP cc_start: 0.6401 (t60) cc_final: 0.6045 (t60) REVERT: C 373 LYS cc_start: 0.5548 (mtpp) cc_final: 0.5147 (mtpp) REVERT: C 382 TYR cc_start: 0.3923 (m-80) cc_final: 0.3606 (m-80) REVERT: C 469 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.5992 (pt) REVERT: D 21 MET cc_start: 0.6496 (mmp) cc_final: 0.5732 (mmm) REVERT: D 60 HIS cc_start: 0.6803 (t-90) cc_final: 0.6422 (t-90) REVERT: D 103 PHE cc_start: 0.6508 (t80) cc_final: 0.6231 (t80) REVERT: D 190 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6434 (tp) REVERT: D 201 TRP cc_start: 0.6519 (t60) cc_final: 0.6081 (t60) REVERT: D 319 THR cc_start: 0.6835 (OUTLIER) cc_final: 0.6488 (p) REVERT: D 382 TYR cc_start: 0.3143 (m-80) cc_final: 0.2671 (m-80) REVERT: D 385 LYS cc_start: 0.6529 (mptp) cc_final: 0.6264 (ptmm) REVERT: D 423 ASP cc_start: 0.6706 (p0) cc_final: 0.6488 (p0) REVERT: E 91 ASN cc_start: 0.4721 (t0) cc_final: 0.4452 (m-40) REVERT: E 321 MET cc_start: 0.4331 (mmp) cc_final: 0.4012 (mmp) REVERT: F 91 ASN cc_start: 0.4995 (t0) cc_final: 0.4596 (m-40) REVERT: F 238 VAL cc_start: 0.5877 (OUTLIER) cc_final: 0.5535 (p) REVERT: G 328 VAL cc_start: 0.7409 (p) cc_final: 0.6968 (t) REVERT: H 327 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6145 (tmt) outliers start: 94 outliers final: 37 residues processed: 469 average time/residue: 0.4458 time to fit residues: 246.4051 Evaluate side-chains 424 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 378 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 189 TYR Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 189 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain E residue 112 PHE Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 112 PHE Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 327 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 58 optimal weight: 3.9990 chunk 227 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 237 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 chunk 236 optimal weight: 0.5980 chunk 186 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN A 448 HIS B 213 HIS B 448 HIS C 213 HIS C 313 GLN D 213 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.237929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.231585 restraints weight = 31783.878| |-----------------------------------------------------------------------------| r_work (start): 0.4708 rms_B_bonded: 0.51 r_work: 0.4633 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.4577 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.4577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5115 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21082 Z= 0.129 Angle : 0.719 17.569 28659 Z= 0.342 Chirality : 0.044 0.230 3441 Planarity : 0.004 0.067 3553 Dihedral : 5.092 56.255 2815 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.44 % Allowed : 26.41 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.21 (0.15), residues: 2623 helix: -0.16 (0.13), residues: 1394 sheet: 1.05 (0.41), residues: 168 loop : -1.94 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 370 TYR 0.028 0.001 TYR B 304 PHE 0.027 0.001 PHE C 312 TRP 0.043 0.002 TRP A 400 HIS 0.005 0.001 HIS D 448 Details of bonding type rmsd covalent geometry : bond 0.00265 (21078) covalent geometry : angle 0.71924 (28651) SS BOND : bond 0.00276 ( 4) SS BOND : angle 0.56510 ( 8) hydrogen bonds : bond 0.04400 ( 1128) hydrogen bonds : angle 5.60072 ( 3270) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 376 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.6491 (mmt) cc_final: 0.5960 (mmm) REVERT: A 47 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6369 (mm) REVERT: A 131 ARG cc_start: 0.6519 (ptm160) cc_final: 0.6279 (ptm160) REVERT: A 143 ILE cc_start: 0.6496 (pt) cc_final: 0.6070 (tp) REVERT: A 201 TRP cc_start: 0.6275 (t60) cc_final: 0.5922 (t60) REVERT: A 220 ILE cc_start: 0.6399 (OUTLIER) cc_final: 0.6018 (mt) REVERT: A 294 LEU cc_start: 0.7636 (mt) cc_final: 0.7389 (mp) REVERT: A 361 ILE cc_start: 0.5456 (mt) cc_final: 0.5165 (tt) REVERT: B 12 LEU cc_start: 0.7084 (tm) cc_final: 0.6482 (pp) REVERT: B 103 PHE cc_start: 0.6633 (t80) cc_final: 0.6411 (t80) REVERT: B 190 LEU cc_start: 0.6651 (tm) cc_final: 0.6054 (mt) REVERT: B 201 TRP cc_start: 0.6753 (t60) cc_final: 0.6462 (t60) REVERT: B 277 ARG cc_start: 0.5056 (ptp90) cc_final: 0.4068 (mtm-85) REVERT: B 382 TYR cc_start: 0.3385 (m-80) cc_final: 0.2680 (m-80) REVERT: C 12 LEU cc_start: 0.6957 (tm) cc_final: 0.6498 (pp) REVERT: C 103 PHE cc_start: 0.6557 (t80) cc_final: 0.6290 (t80) REVERT: C 120 LEU cc_start: 0.5968 (OUTLIER) cc_final: 0.5658 (tt) REVERT: C 201 TRP cc_start: 0.6446 (t60) cc_final: 0.6119 (t60) REVERT: C 373 LYS cc_start: 0.5565 (mtpp) cc_final: 0.5076 (mtpp) REVERT: C 382 TYR cc_start: 0.4049 (m-80) cc_final: 0.3712 (m-80) REVERT: C 469 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.5868 (pt) REVERT: D 21 MET cc_start: 0.6491 (mmp) cc_final: 0.5805 (mmm) REVERT: D 60 HIS cc_start: 0.6780 (t-90) cc_final: 0.6395 (t-90) REVERT: D 103 PHE cc_start: 0.6452 (t80) cc_final: 0.6170 (t80) REVERT: D 205 MET cc_start: 0.3729 (pmm) cc_final: 0.3395 (ptp) REVERT: D 385 LYS cc_start: 0.6579 (mptp) cc_final: 0.6287 (ptmm) REVERT: F 91 ASN cc_start: 0.4799 (t0) cc_final: 0.4556 (m-40) REVERT: G 326 VAL cc_start: 0.7359 (OUTLIER) cc_final: 0.7098 (t) REVERT: G 327 MET cc_start: 0.6498 (OUTLIER) cc_final: 0.6013 (tmt) REVERT: H 327 MET cc_start: 0.6481 (OUTLIER) cc_final: 0.6069 (tmt) REVERT: H 328 VAL cc_start: 0.7264 (p) cc_final: 0.7005 (t) outliers start: 75 outliers final: 49 residues processed: 430 average time/residue: 0.4658 time to fit residues: 235.1445 Evaluate side-chains 409 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 353 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 189 TYR Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain E residue 112 PHE Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 112 PHE Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 327 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 257 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 127 optimal weight: 0.0020 chunk 76 optimal weight: 0.0770 chunk 183 optimal weight: 5.9990 chunk 198 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 168 optimal weight: 0.8980 chunk 242 optimal weight: 4.9990 chunk 226 optimal weight: 0.9980 overall best weight: 0.5546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN A 448 HIS B 213 HIS B 448 HIS C 213 HIS D 213 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.239693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.233455 restraints weight = 31914.059| |-----------------------------------------------------------------------------| r_work (start): 0.4724 rms_B_bonded: 0.51 r_work: 0.4654 rms_B_bonded: 1.03 restraints_weight: 0.5000 r_work: 0.4602 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.4602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5052 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21082 Z= 0.123 Angle : 0.726 17.689 28659 Z= 0.343 Chirality : 0.043 0.220 3441 Planarity : 0.004 0.069 3553 Dihedral : 4.941 56.143 2814 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.21 % Allowed : 26.73 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.08 (0.15), residues: 2623 helix: -0.04 (0.13), residues: 1395 sheet: 1.09 (0.41), residues: 168 loop : -1.92 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 8 TYR 0.028 0.001 TYR B 304 PHE 0.045 0.001 PHE C 312 TRP 0.038 0.002 TRP A 400 HIS 0.004 0.001 HIS D 448 Details of bonding type rmsd covalent geometry : bond 0.00257 (21078) covalent geometry : angle 0.72630 (28651) SS BOND : bond 0.00302 ( 4) SS BOND : angle 0.82777 ( 8) hydrogen bonds : bond 0.04184 ( 1128) hydrogen bonds : angle 5.45535 ( 3270) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 376 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.6372 (mmt) cc_final: 0.6019 (mmm) REVERT: A 47 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.6213 (mp) REVERT: A 131 ARG cc_start: 0.6027 (ptm160) cc_final: 0.5808 (ptm160) REVERT: A 143 ILE cc_start: 0.6424 (pt) cc_final: 0.6012 (tp) REVERT: A 190 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.6010 (tt) REVERT: A 201 TRP cc_start: 0.6206 (t60) cc_final: 0.5876 (t60) REVERT: A 220 ILE cc_start: 0.6295 (OUTLIER) cc_final: 0.5929 (mt) REVERT: A 319 THR cc_start: 0.7449 (OUTLIER) cc_final: 0.7159 (p) REVERT: A 361 ILE cc_start: 0.5410 (mt) cc_final: 0.5130 (tt) REVERT: A 379 ARG cc_start: 0.6960 (ptp-110) cc_final: 0.6544 (ttm-80) REVERT: A 381 VAL cc_start: 0.7403 (m) cc_final: 0.6638 (t) REVERT: A 382 TYR cc_start: 0.3775 (m-80) cc_final: 0.2524 (t80) REVERT: A 478 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6481 (mp) REVERT: B 12 LEU cc_start: 0.6918 (tm) cc_final: 0.6427 (pp) REVERT: B 103 PHE cc_start: 0.6550 (t80) cc_final: 0.6347 (t80) REVERT: B 190 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6021 (mt) REVERT: B 201 TRP cc_start: 0.6421 (t60) cc_final: 0.6161 (t60) REVERT: B 277 ARG cc_start: 0.5061 (ptp90) cc_final: 0.4119 (mtm-85) REVERT: B 381 VAL cc_start: 0.6927 (m) cc_final: 0.6427 (t) REVERT: C 12 LEU cc_start: 0.6912 (tm) cc_final: 0.6450 (pp) REVERT: C 103 PHE cc_start: 0.6563 (t80) cc_final: 0.6255 (t80) REVERT: C 120 LEU cc_start: 0.5783 (OUTLIER) cc_final: 0.5538 (tt) REVERT: C 201 TRP cc_start: 0.6405 (t60) cc_final: 0.6068 (t60) REVERT: C 373 LYS cc_start: 0.5331 (mtpp) cc_final: 0.4861 (mtpp) REVERT: C 469 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.5962 (pt) REVERT: D 21 MET cc_start: 0.6496 (mmp) cc_final: 0.6002 (mmm) REVERT: D 60 HIS cc_start: 0.6666 (t-90) cc_final: 0.6306 (t-90) REVERT: D 103 PHE cc_start: 0.6451 (t80) cc_final: 0.6165 (t80) REVERT: D 385 LYS cc_start: 0.6255 (mptp) cc_final: 0.6037 (ptmm) REVERT: E 301 PHE cc_start: 0.6333 (OUTLIER) cc_final: 0.5986 (t80) REVERT: F 91 ASN cc_start: 0.4781 (t0) cc_final: 0.4556 (m-40) REVERT: G 327 MET cc_start: 0.6500 (OUTLIER) cc_final: 0.5823 (tmt) REVERT: G 328 VAL cc_start: 0.7412 (p) cc_final: 0.6854 (t) REVERT: H 91 ASN cc_start: 0.4716 (t0) cc_final: 0.4429 (m-40) REVERT: H 327 MET cc_start: 0.6414 (OUTLIER) cc_final: 0.6030 (tmt) outliers start: 70 outliers final: 42 residues processed: 426 average time/residue: 0.4378 time to fit residues: 219.2504 Evaluate side-chains 409 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 356 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 189 TYR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain E residue 112 PHE Chi-restraints excluded: chain E residue 301 PHE Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 112 PHE Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 327 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 184 optimal weight: 0.0030 chunk 74 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 192 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 237 optimal weight: 6.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 HIS A 436 ASN A 448 HIS B 213 HIS B 448 HIS B 453 ASN C 213 HIS C 313 GLN D 213 HIS D 377 HIS H 18 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.240084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.234005 restraints weight = 31934.638| |-----------------------------------------------------------------------------| r_work (start): 0.4733 rms_B_bonded: 0.51 r_work: 0.4650 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.4560 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.4560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5064 moved from start: 0.5705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21082 Z= 0.125 Angle : 0.728 17.987 28659 Z= 0.343 Chirality : 0.043 0.204 3441 Planarity : 0.004 0.069 3553 Dihedral : 4.883 55.827 2814 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.98 % Allowed : 27.46 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.02 (0.15), residues: 2623 helix: -0.00 (0.13), residues: 1398 sheet: 1.10 (0.41), residues: 168 loop : -1.88 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 8 TYR 0.027 0.002 TYR B 304 PHE 0.037 0.001 PHE A 133 TRP 0.037 0.002 TRP A 400 HIS 0.006 0.001 HIS D 448 Details of bonding type rmsd covalent geometry : bond 0.00264 (21078) covalent geometry : angle 0.72820 (28651) SS BOND : bond 0.00286 ( 4) SS BOND : angle 0.63379 ( 8) hydrogen bonds : bond 0.04190 ( 1128) hydrogen bonds : angle 5.41477 ( 3270) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6819.32 seconds wall clock time: 116 minutes 56.49 seconds (7016.49 seconds total)