Starting phenix.real_space_refine on Wed Mar 4 22:11:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nd2_12273/03_2026/7nd2_12273.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nd2_12273/03_2026/7nd2_12273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nd2_12273/03_2026/7nd2_12273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nd2_12273/03_2026/7nd2_12273.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nd2_12273/03_2026/7nd2_12273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nd2_12273/03_2026/7nd2_12273.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 10670 2.51 5 N 2894 2.21 5 O 3168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 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: 16824 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2565 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 13, 'TRANS': 316} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2721 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 335} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'HIS:plan': 3, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 1563 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 210, 1553 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} Conformer: "B" Number of residues, atoms: 210, 1553 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} bond proxies already assigned to first conformer: 1576 Chain: "F" Number of atoms: 1563 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 210, 1553 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} Conformer: "B" Number of residues, atoms: 210, 1553 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} bond proxies already assigned to first conformer: 1576 Chain: "D" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2721 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 335} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'HIS:plan': 3, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2565 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 13, 'TRANS': 316} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 1563 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 210, 1553 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} Conformer: "B" Number of residues, atoms: 210, 1553 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} bond proxies already assigned to first conformer: 1576 Chain: "G" Number of atoms: 1563 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 210, 1553 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} Conformer: "B" Number of residues, atoms: 210, 1553 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} bond proxies already assigned to first conformer: 1576 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AHIS E 195 " occ=0.42 ... (18 atoms not shown) pdb=" NE2BHIS E 195 " occ=0.58 residue: pdb=" N AHIS F 195 " occ=0.42 ... (18 atoms not shown) pdb=" NE2BHIS F 195 " occ=0.58 residue: pdb=" N AHIS H 195 " occ=0.42 ... (18 atoms not shown) pdb=" NE2BHIS H 195 " occ=0.58 residue: pdb=" N AHIS G 195 " occ=0.42 ... (18 atoms not shown) pdb=" NE2BHIS G 195 " occ=0.58 Time building chain proxies: 4.94, per 1000 atoms: 0.29 Number of scatterers: 16824 At special positions: 0 Unit cell: (180.36, 102.6, 128.52, 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 92 16.00 O 3168 8.00 N 2894 7.00 C 10670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 1.1 seconds 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4172 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 15 sheets defined 55.2% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 219 through 226 removed outlier: 3.905A pdb=" N ASN A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.936A pdb=" N LEU A 239 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 265 removed outlier: 3.966A pdb=" N GLN A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 284 removed outlier: 4.013A pdb=" N ALA A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 306 removed outlier: 3.997A pdb=" N GLN A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 306 " --> pdb=" O GLN A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 325 Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 335 through 370 removed outlier: 3.673A pdb=" N LEU A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) Proline residue: A 358 - end of helix Processing helix chain 'A' and resid 374 through 406 removed outlier: 3.610A pdb=" N ARG A 378 " --> pdb=" O THR A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 455 removed outlier: 4.773A pdb=" N THR A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A 427 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP A 436 " --> pdb=" O HIS A 432 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 499 removed outlier: 4.247A pdb=" N CYS A 468 " --> pdb=" O THR A 464 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASP A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N TYR A 493 " --> pdb=" O ASN A 489 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 499 " --> pdb=" O ILE A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 513 through 532 Processing helix chain 'A' and resid 540 through 552 removed outlier: 4.477A pdb=" N ALA A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 118 through 138 removed outlier: 5.041A pdb=" N ARG C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 168 removed outlier: 4.123A pdb=" N ILE C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 187 Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 244 through 251 Processing helix chain 'C' and resid 268 through 279 Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 296 through 314 Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 328 through 339 removed outlier: 4.341A pdb=" N ALA C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 39 removed outlier: 3.775A pdb=" N THR E 37 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA E 38 " --> pdb=" O MET E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 49 removed outlier: 3.864A pdb=" N LYS E 49 " --> pdb=" O PRO E 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 46 through 49' Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 82 through 86 removed outlier: 3.622A pdb=" N ARG E 85 " --> pdb=" O ASP E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 99 removed outlier: 3.599A pdb=" N LEU E 98 " --> pdb=" O PRO E 95 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR E 99 " --> pdb=" O GLY E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 103 Processing helix chain 'E' and resid 104 through 117 Processing helix chain 'E' and resid 126 through 134 removed outlier: 3.603A pdb=" N ALA E 134 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 159 removed outlier: 3.851A pdb=" N LEU E 156 " --> pdb=" O SER E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 176 removed outlier: 3.688A pdb=" N LYS E 174 " --> pdb=" O GLU E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 216 removed outlier: 3.698A pdb=" N ALA E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL E 209 " --> pdb=" O THR E 205 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN E 210 " --> pdb=" O VAL E 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 39 removed outlier: 3.815A pdb=" N MET F 34 " --> pdb=" O HIS F 30 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA F 35 " --> pdb=" O CYS F 31 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA F 38 " --> pdb=" O MET F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 49 removed outlier: 3.647A pdb=" N LYS F 49 " --> pdb=" O PRO F 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 46 through 49' Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 82 through 86 removed outlier: 3.797A pdb=" N ARG F 85 " --> pdb=" O ASP F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 99 removed outlier: 4.615A pdb=" N LEU F 98 " --> pdb=" O PRO F 95 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR F 99 " --> pdb=" O GLY F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 103 Processing helix chain 'F' and resid 104 through 118 Processing helix chain 'F' and resid 126 through 134 removed outlier: 3.805A pdb=" N CYS F 133 " --> pdb=" O ALA F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 158 removed outlier: 3.838A pdb=" N ARG F 158 " --> pdb=" O CYS F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 176 removed outlier: 3.735A pdb=" N VAL F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU F 170 " --> pdb=" O PRO F 166 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL F 173 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER F 176 " --> pdb=" O PHE F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 216 removed outlier: 3.802A pdb=" N ALA F 208 " --> pdb=" O SER F 204 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN F 210 " --> pdb=" O VAL F 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 118 through 138 removed outlier: 5.043A pdb=" N ARG D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 168 removed outlier: 4.130A pdb=" N ILE D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 244 through 251 Processing helix chain 'D' and resid 268 through 279 Processing helix chain 'D' and resid 288 through 293 Processing helix chain 'D' and resid 296 through 314 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 328 through 339 removed outlier: 4.335A pdb=" N ALA D 335 " --> pdb=" O VAL D 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 226 removed outlier: 3.919A pdb=" N ASN B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.935A pdb=" N LEU B 239 " --> pdb=" O GLN B 235 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.966A pdb=" N GLN B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 284 removed outlier: 4.010A pdb=" N ALA B 269 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 306 removed outlier: 3.852A pdb=" N GLN B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU B 306 " --> pdb=" O GLN B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 325 Proline residue: B 313 - end of helix Processing helix chain 'B' and resid 335 through 370 removed outlier: 3.677A pdb=" N LEU B 339 " --> pdb=" O THR B 335 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) Proline residue: B 358 - end of helix Processing helix chain 'B' and resid 374 through 407 removed outlier: 3.606A pdb=" N ARG B 378 " --> pdb=" O THR B 374 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 455 removed outlier: 4.547A pdb=" N THR B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP B 436 " --> pdb=" O HIS B 432 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN B 447 " --> pdb=" O LYS B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 499 removed outlier: 4.207A pdb=" N CYS B 468 " --> pdb=" O THR B 464 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N TYR B 493 " --> pdb=" O ASN B 489 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 499 " --> pdb=" O ILE B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 513 through 532 Processing helix chain 'B' and resid 540 through 552 removed outlier: 4.475A pdb=" N ALA B 546 " --> pdb=" O GLU B 542 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 39 removed outlier: 3.852A pdb=" N MET H 34 " --> pdb=" O HIS H 30 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA H 35 " --> pdb=" O CYS H 31 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR H 37 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA H 38 " --> pdb=" O MET H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 49 removed outlier: 3.660A pdb=" N LYS H 49 " --> pdb=" O PRO H 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 46 through 49' Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 82 through 86 removed outlier: 3.765A pdb=" N ARG H 85 " --> pdb=" O ASP H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 99 removed outlier: 4.598A pdb=" N LEU H 98 " --> pdb=" O PRO H 95 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR H 99 " --> pdb=" O GLY H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 103 Processing helix chain 'H' and resid 104 through 118 Processing helix chain 'H' and resid 126 through 134 removed outlier: 3.801A pdb=" N CYS H 133 " --> pdb=" O ALA H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 158 removed outlier: 3.817A pdb=" N ARG H 158 " --> pdb=" O CYS H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 176 removed outlier: 3.668A pdb=" N VAL H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU H 170 " --> pdb=" O PRO H 166 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL H 173 " --> pdb=" O VAL H 169 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER H 176 " --> pdb=" O PHE H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 216 removed outlier: 3.855A pdb=" N ALA H 208 " --> pdb=" O SER H 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 39 removed outlier: 3.770A pdb=" N THR G 37 " --> pdb=" O THR G 33 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA G 38 " --> pdb=" O MET G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 49 removed outlier: 3.886A pdb=" N LYS G 49 " --> pdb=" O PRO G 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 46 through 49' Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 82 through 84 No H-bonds generated for 'chain 'G' and resid 82 through 84' Processing helix chain 'G' and resid 94 through 99 removed outlier: 3.587A pdb=" N LEU G 98 " --> pdb=" O PRO G 95 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR G 99 " --> pdb=" O GLY G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 103 Processing helix chain 'G' and resid 104 through 117 Processing helix chain 'G' and resid 126 through 134 removed outlier: 3.607A pdb=" N ALA G 134 " --> pdb=" O LEU G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 159 removed outlier: 3.794A pdb=" N LEU G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 176 removed outlier: 3.775A pdb=" N LYS G 174 " --> pdb=" O GLU G 170 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP G 175 " --> pdb=" O ASP G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 216 removed outlier: 3.701A pdb=" N ALA G 208 " --> pdb=" O SER G 204 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL G 209 " --> pdb=" O THR G 205 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN G 210 " --> pdb=" O VAL G 206 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 0 through 3 Processing sheet with id=AA2, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AA3, first strand: chain 'C' and resid 102 through 106 removed outlier: 6.800A pdb=" N LYS C 34 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA C 67 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N CYS C 40 " --> pdb=" O GLU C 65 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU C 65 " --> pdb=" O CYS C 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 102 through 106 Processing sheet with id=AA5, first strand: chain 'C' and resid 194 through 197 removed outlier: 6.779A pdb=" N VAL C 172 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE C 196 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N SER C 174 " --> pdb=" O ILE C 196 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER C 147 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL C 218 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY C 255 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE C 220 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N HIS C 257 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU C 222 " --> pdb=" O HIS C 257 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL C 259 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N THR C 281 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY C 256 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ALA C 283 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TRP C 258 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N THR D 281 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLY D 256 " --> pdb=" O THR D 281 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ALA D 283 " --> pdb=" O GLY D 256 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TRP D 258 " --> pdb=" O ALA D 283 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL D 218 " --> pdb=" O GLY D 253 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLY D 255 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE D 220 " --> pdb=" O GLY D 255 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N HIS D 257 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU D 222 " --> pdb=" O HIS D 257 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL D 259 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER D 147 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D 172 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE D 196 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N SER D 174 " --> pdb=" O ILE D 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 76 through 77 removed outlier: 6.824A pdb=" N ALA E 11 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU E 90 " --> pdb=" O ALA E 11 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU E 13 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE E 121 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N GLY E 199 " --> pdb=" O ILE E 121 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA E 123 " --> pdb=" O GLY E 199 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU E 196 " --> pdb=" O ASP E 193 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU F 89 " --> pdb=" O CYS F 122 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL F 124 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE F 91 " --> pdb=" O VAL F 124 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA F 11 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LEU F 90 " --> pdb=" O ALA F 11 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU F 13 " --> pdb=" O LEU F 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 23 through 24 removed outlier: 6.121A pdb=" N VAL E 23 " --> pdb=" O VAL E 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 23 through 24 removed outlier: 5.429A pdb=" N VAL F 23 " --> pdb=" O VAL F 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 0 through 3 Processing sheet with id=AB1, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 102 through 106 removed outlier: 6.803A pdb=" N LYS D 34 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA D 67 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N CYS D 40 " --> pdb=" O GLU D 65 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLU D 65 " --> pdb=" O CYS D 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 102 through 106 Processing sheet with id=AB4, first strand: chain 'H' and resid 76 through 77 removed outlier: 7.139A pdb=" N ALA H 11 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N LEU H 90 " --> pdb=" O ALA H 11 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU H 13 " --> pdb=" O LEU H 90 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU H 89 " --> pdb=" O CYS H 122 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL H 124 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE H 91 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU G 196 " --> pdb=" O ASP G 193 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE G 121 " --> pdb=" O VAL G 197 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N GLY G 199 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA G 123 " --> pdb=" O GLY G 199 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA G 11 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N LEU G 90 " --> pdb=" O ALA G 11 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU G 13 " --> pdb=" O LEU G 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 23 through 24 removed outlier: 5.637A pdb=" N VAL H 23 " --> pdb=" O VAL H 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 23 through 24 removed outlier: 5.984A pdb=" N VAL G 23 " --> pdb=" O VAL G 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 874 hydrogen bonds defined for protein. 2505 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: 2.76 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4863 1.33 - 1.46: 3702 1.46 - 1.58: 8473 1.58 - 1.70: 4 1.70 - 1.83: 124 Bond restraints: 17166 Sorted by residual: bond pdb=" CG PRO G 92 " pdb=" CD PRO G 92 " ideal model delta sigma weight residual 1.503 1.212 0.291 3.40e-02 8.65e+02 7.35e+01 bond pdb=" N PRO G 92 " pdb=" CD PRO G 92 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.93e+01 bond pdb=" CG1 ILE B 350 " pdb=" CD1 ILE B 350 " ideal model delta sigma weight residual 1.513 1.368 0.145 3.90e-02 6.57e+02 1.38e+01 bond pdb=" CG1 ILE A 350 " pdb=" CD1 ILE A 350 " ideal model delta sigma weight residual 1.513 1.375 0.138 3.90e-02 6.57e+02 1.26e+01 bond pdb=" CB PRO G 92 " pdb=" CG PRO G 92 " ideal model delta sigma weight residual 1.492 1.653 -0.161 5.00e-02 4.00e+02 1.04e+01 ... (remaining 17161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 22576 4.17 - 8.34: 646 8.34 - 12.52: 75 12.52 - 16.69: 11 16.69 - 20.86: 4 Bond angle restraints: 23312 Sorted by residual: angle pdb=" N PRO G 92 " pdb=" CD PRO G 92 " pdb=" CG PRO G 92 " ideal model delta sigma weight residual 103.20 87.80 15.40 1.50e+00 4.44e-01 1.05e+02 angle pdb=" CA GLU E 21 " pdb=" CB GLU E 21 " pdb=" CG GLU E 21 " ideal model delta sigma weight residual 114.10 131.62 -17.52 2.00e+00 2.50e-01 7.67e+01 angle pdb=" CA PRO G 92 " pdb=" N PRO G 92 " pdb=" CD PRO G 92 " ideal model delta sigma weight residual 112.00 100.04 11.96 1.40e+00 5.10e-01 7.30e+01 angle pdb=" CA GLU G 21 " pdb=" CB GLU G 21 " pdb=" CG GLU G 21 " ideal model delta sigma weight residual 114.10 130.06 -15.96 2.00e+00 2.50e-01 6.37e+01 angle pdb=" CA ARG F 164 " pdb=" CB ARG F 164 " pdb=" CG ARG F 164 " ideal model delta sigma weight residual 114.10 129.25 -15.15 2.00e+00 2.50e-01 5.74e+01 ... (remaining 23307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 9367 17.87 - 35.75: 833 35.75 - 53.62: 111 53.62 - 71.50: 27 71.50 - 89.37: 10 Dihedral angle restraints: 10348 sinusoidal: 3922 harmonic: 6426 Sorted by residual: dihedral pdb=" CA LYS H 70 " pdb=" C LYS H 70 " pdb=" N ALA H 71 " pdb=" CA ALA H 71 " ideal model delta harmonic sigma weight residual 180.00 -148.47 -31.53 0 5.00e+00 4.00e-02 3.98e+01 dihedral pdb=" CA LYS F 70 " pdb=" C LYS F 70 " pdb=" N ALA F 71 " pdb=" CA ALA F 71 " ideal model delta harmonic sigma weight residual -180.00 -149.41 -30.59 0 5.00e+00 4.00e-02 3.74e+01 dihedral pdb=" CA PRO H 151 " pdb=" C PRO H 151 " pdb=" N SER H 152 " pdb=" CA SER H 152 " ideal model delta harmonic sigma weight residual 180.00 154.74 25.26 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 10345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1991 0.081 - 0.163: 538 0.163 - 0.244: 155 0.244 - 0.326: 25 0.326 - 0.407: 11 Chirality restraints: 2720 Sorted by residual: chirality pdb=" CB VAL E 173 " pdb=" CA VAL E 173 " pdb=" CG1 VAL E 173 " pdb=" CG2 VAL E 173 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" CG LEU E 167 " pdb=" CB LEU E 167 " pdb=" CD1 LEU E 167 " pdb=" CD2 LEU E 167 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CG LEU H 98 " pdb=" CB LEU H 98 " pdb=" CD1 LEU H 98 " pdb=" CD2 LEU H 98 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.40e+00 ... (remaining 2717 not shown) Planarity restraints: 3004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 91 " -0.121 5.00e-02 4.00e+02 1.72e-01 4.71e+01 pdb=" N PRO G 92 " 0.296 5.00e-02 4.00e+02 pdb=" CA PRO G 92 " -0.093 5.00e-02 4.00e+02 pdb=" CD PRO G 92 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 159 " 0.100 5.00e-02 4.00e+02 1.49e-01 3.54e+01 pdb=" N PRO G 160 " -0.257 5.00e-02 4.00e+02 pdb=" CA PRO G 160 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO G 160 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 141 " -0.033 2.00e-02 2.50e+03 3.19e-02 2.55e+01 pdb=" CG TRP H 141 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 TRP H 141 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP H 141 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP H 141 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 141 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP H 141 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 141 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 141 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP H 141 " -0.012 2.00e-02 2.50e+03 ... (remaining 3001 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1088 2.72 - 3.26: 18236 3.26 - 3.81: 28737 3.81 - 4.35: 35152 4.35 - 4.90: 56634 Nonbonded interactions: 139847 Sorted by model distance: nonbonded pdb=" O LEU B 333 " pdb=" OG1 THR B 336 " model vdw 2.172 3.040 nonbonded pdb=" O LEU A 333 " pdb=" OG1 THR A 336 " model vdw 2.176 3.040 nonbonded pdb=" O LYS B 340 " pdb=" OG SER B 343 " model vdw 2.216 3.040 nonbonded pdb=" O LYS A 340 " pdb=" OG SER A 343 " model vdw 2.217 3.040 nonbonded pdb=" O TYR B 493 " pdb=" OG SER B 497 " model vdw 2.224 3.040 ... (remaining 139842 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 8 through 194 or resid 196 through 217)) selection = (chain 'F' and (resid 8 through 194 or resid 196 through 217)) selection = (chain 'G' and (resid 8 through 194 or resid 196 through 217)) selection = (chain 'H' and (resid 8 through 194 or resid 196 through 217)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.280 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 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 0.291 17166 Z= 0.494 Angle : 1.654 20.859 23312 Z= 0.890 Chirality : 0.085 0.407 2720 Planarity : 0.011 0.172 3004 Dihedral : 13.917 89.373 6176 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.99 % Favored : 94.69 % Rotamer: Outliers : 0.22 % Allowed : 0.60 % Favored : 99.18 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.95 (0.16), residues: 2196 helix: 0.09 (0.14), residues: 1024 sheet: 0.28 (0.34), residues: 210 loop : -1.60 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.055 0.003 ARG F 164 TYR 0.058 0.006 TYR B 233 PHE 0.044 0.005 PHE B 395 TRP 0.081 0.008 TRP H 141 HIS 0.030 0.004 HIS E 30 Details of bonding type rmsd covalent geometry : bond 0.01114 (17166) covalent geometry : angle 1.65436 (23312) hydrogen bonds : bond 0.17776 ( 866) hydrogen bonds : angle 7.39820 ( 2505) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 ASP cc_start: 0.8544 (m-30) cc_final: 0.8182 (t0) REVERT: A 545 LEU cc_start: 0.7806 (pp) cc_final: 0.7147 (tp) REVERT: C 92 LEU cc_start: 0.8809 (tp) cc_final: 0.8573 (tp) REVERT: E 29 LEU cc_start: 0.7957 (tt) cc_final: 0.7081 (mm) REVERT: E 34 MET cc_start: 0.8319 (ptt) cc_final: 0.7494 (ptp) REVERT: E 155 GLU cc_start: 0.8401 (pt0) cc_final: 0.8092 (pt0) REVERT: F 34 MET cc_start: 0.6024 (tmm) cc_final: 0.5661 (ptt) REVERT: F 138 ASP cc_start: 0.8610 (p0) cc_final: 0.8156 (p0) REVERT: F 139 ARG cc_start: 0.7392 (ttp80) cc_final: 0.5967 (mmm160) REVERT: F 143 PHE cc_start: 0.8552 (m-80) cc_final: 0.7988 (m-80) REVERT: F 164 ARG cc_start: 0.8421 (tpt170) cc_final: 0.8148 (mpp-170) REVERT: D 92 LEU cc_start: 0.8824 (tp) cc_final: 0.8565 (tp) REVERT: D 265 LEU cc_start: 0.8882 (tp) cc_final: 0.8666 (tt) REVERT: B 439 LYS cc_start: 0.8929 (mmtp) cc_final: 0.8429 (tptp) REVERT: B 440 ASP cc_start: 0.8355 (m-30) cc_final: 0.7996 (t0) REVERT: B 545 LEU cc_start: 0.7926 (pp) cc_final: 0.7348 (tp) REVERT: H 34 MET cc_start: 0.5952 (tmm) cc_final: 0.5580 (ptt) REVERT: H 51 MET cc_start: 0.4681 (mtt) cc_final: 0.4377 (mtt) REVERT: H 138 ASP cc_start: 0.8638 (p0) cc_final: 0.8153 (p0) REVERT: H 139 ARG cc_start: 0.7418 (ttp80) cc_final: 0.5987 (mmm160) REVERT: H 143 PHE cc_start: 0.8581 (m-80) cc_final: 0.8053 (m-80) REVERT: G 34 MET cc_start: 0.8331 (ptm) cc_final: 0.7768 (ptp) REVERT: G 94 CYS cc_start: 0.7779 (p) cc_final: 0.7576 (p) REVERT: G 155 GLU cc_start: 0.8428 (pt0) cc_final: 0.7876 (pt0) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.1545 time to fit residues: 52.4045 Evaluate side-chains 157 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 HIS C 296 GLN C 345 GLN ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS F 189 HIS ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS D 296 GLN D 345 GLN B 249 GLN H 113 HIS ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.111525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.083834 restraints weight = 133688.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.084947 restraints weight = 72656.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.085917 restraints weight = 49693.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.086419 restraints weight = 37203.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.086760 restraints weight = 34991.476| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 17166 Z= 0.313 Angle : 0.921 12.539 23312 Z= 0.482 Chirality : 0.049 0.228 2720 Planarity : 0.007 0.093 3004 Dihedral : 6.070 35.419 2336 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.71 % Favored : 96.11 % Rotamer: Outliers : 1.48 % Allowed : 10.53 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.86 (0.17), residues: 2196 helix: 0.11 (0.15), residues: 1048 sheet: 0.24 (0.31), residues: 232 loop : -1.55 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 62 TYR 0.027 0.003 TYR B 420 PHE 0.029 0.003 PHE E 172 TRP 0.033 0.004 TRP E 63 HIS 0.016 0.002 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00664 (17166) covalent geometry : angle 0.92132 (23312) hydrogen bonds : bond 0.05902 ( 866) hydrogen bonds : angle 6.08835 ( 2505) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.678 Fit side-chains REVERT: A 440 ASP cc_start: 0.8695 (m-30) cc_final: 0.8348 (t0) REVERT: C 92 LEU cc_start: 0.8884 (tp) cc_final: 0.8592 (tp) REVERT: E 34 MET cc_start: 0.8597 (ptt) cc_final: 0.7999 (ptp) REVERT: E 155 GLU cc_start: 0.8215 (pt0) cc_final: 0.7180 (pm20) REVERT: F 34 MET cc_start: 0.6583 (tmm) cc_final: 0.6043 (ptp) REVERT: F 143 PHE cc_start: 0.8922 (m-80) cc_final: 0.8331 (m-80) REVERT: F 164 ARG cc_start: 0.8465 (tpt170) cc_final: 0.8147 (mpp-170) REVERT: D 92 LEU cc_start: 0.8899 (tp) cc_final: 0.8593 (tp) REVERT: D 265 LEU cc_start: 0.9077 (tp) cc_final: 0.8875 (tt) REVERT: B 439 LYS cc_start: 0.8954 (mmtp) cc_final: 0.8621 (mmtp) REVERT: B 440 ASP cc_start: 0.8589 (m-30) cc_final: 0.8268 (t0) REVERT: B 545 LEU cc_start: 0.7834 (pp) cc_final: 0.7119 (tp) REVERT: H 34 MET cc_start: 0.6124 (tmm) cc_final: 0.5400 (ptp) REVERT: H 51 MET cc_start: 0.5611 (mtt) cc_final: 0.4951 (mtt) REVERT: H 143 PHE cc_start: 0.9061 (m-80) cc_final: 0.8367 (m-80) REVERT: G 34 MET cc_start: 0.8507 (ptm) cc_final: 0.8036 (mtt) outliers start: 27 outliers final: 18 residues processed: 186 average time/residue: 0.1403 time to fit residues: 38.8664 Evaluate side-chains 153 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 115 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 84 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 195 optimal weight: 9.9990 chunk 218 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 211 optimal weight: 0.0010 chunk 77 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 79 optimal weight: 40.0000 chunk 39 optimal weight: 0.4980 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN C 345 GLN E 210 GLN F 113 HIS ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 GLN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 GLN B 419 ASN H 113 HIS ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.114448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.087414 restraints weight = 144182.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.088689 restraints weight = 73613.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.089516 restraints weight = 54611.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.089648 restraints weight = 44586.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.090625 restraints weight = 38358.535| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3765 r_free = 0.3765 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3765 r_free = 0.3765 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17166 Z= 0.155 Angle : 0.752 11.833 23312 Z= 0.386 Chirality : 0.045 0.255 2720 Planarity : 0.005 0.071 3004 Dihedral : 5.592 42.392 2336 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.08 % Favored : 95.65 % Rotamer: Outliers : 1.81 % Allowed : 13.82 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.63 (0.17), residues: 2196 helix: 0.34 (0.15), residues: 1056 sheet: 0.06 (0.31), residues: 236 loop : -1.41 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 62 TYR 0.018 0.002 TYR A 303 PHE 0.022 0.002 PHE H 114 TRP 0.021 0.003 TRP G 63 HIS 0.018 0.001 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00336 (17166) covalent geometry : angle 0.75228 (23312) hydrogen bonds : bond 0.04801 ( 866) hydrogen bonds : angle 5.46679 ( 2505) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 MET cc_start: 0.8095 (mmt) cc_final: 0.7842 (mmm) REVERT: A 440 ASP cc_start: 0.8527 (m-30) cc_final: 0.8309 (t0) REVERT: A 444 HIS cc_start: 0.8782 (t-170) cc_final: 0.8304 (t-170) REVERT: A 453 HIS cc_start: 0.7693 (OUTLIER) cc_final: 0.7435 (t70) REVERT: C 92 LEU cc_start: 0.8739 (tp) cc_final: 0.8537 (tp) REVERT: E 29 LEU cc_start: 0.8239 (tt) cc_final: 0.7373 (mm) REVERT: E 34 MET cc_start: 0.8453 (ptt) cc_final: 0.7836 (mtt) REVERT: E 144 ASP cc_start: 0.7866 (p0) cc_final: 0.7349 (m-30) REVERT: E 155 GLU cc_start: 0.7976 (pt0) cc_final: 0.6989 (pm20) REVERT: F 34 MET cc_start: 0.6725 (tmm) cc_final: 0.6299 (ptp) REVERT: F 51 MET cc_start: 0.5413 (mtt) cc_final: 0.4868 (mtt) REVERT: F 143 PHE cc_start: 0.8754 (m-80) cc_final: 0.8270 (m-80) REVERT: D 92 LEU cc_start: 0.8787 (tp) cc_final: 0.8561 (tp) REVERT: B 439 LYS cc_start: 0.8924 (mmtp) cc_final: 0.8381 (tptp) REVERT: B 517 MET cc_start: 0.8629 (tmm) cc_final: 0.8423 (tmm) REVERT: B 545 LEU cc_start: 0.7808 (pp) cc_final: 0.7095 (tp) REVERT: H 34 MET cc_start: 0.6154 (tmm) cc_final: 0.5515 (ptp) REVERT: H 51 MET cc_start: 0.5722 (mtt) cc_final: 0.5039 (mtt) REVERT: H 143 PHE cc_start: 0.9027 (m-80) cc_final: 0.8322 (m-80) REVERT: H 194 ARG cc_start: 0.8368 (tpp-160) cc_final: 0.8124 (tpp-160) REVERT: G 34 MET cc_start: 0.8432 (ptm) cc_final: 0.7987 (mtt) outliers start: 33 outliers final: 16 residues processed: 210 average time/residue: 0.1415 time to fit residues: 43.8671 Evaluate side-chains 166 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain H residue 85 ARG Chi-restraints excluded: chain G residue 115 HIS Chi-restraints excluded: chain G residue 171 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 86 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 144 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN E 115 HIS F 113 HIS ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 HIS ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.112332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.084339 restraints weight = 139380.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.086103 restraints weight = 73245.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.087043 restraints weight = 49960.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.086964 restraints weight = 38800.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.087356 restraints weight = 37098.246| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17166 Z= 0.220 Angle : 0.761 11.334 23312 Z= 0.392 Chirality : 0.045 0.202 2720 Planarity : 0.005 0.064 3004 Dihedral : 5.530 41.166 2336 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.80 % Favored : 95.92 % Rotamer: Outliers : 3.02 % Allowed : 15.46 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.61 (0.17), residues: 2196 helix: 0.33 (0.15), residues: 1050 sheet: -0.05 (0.33), residues: 240 loop : -1.32 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 164 TYR 0.029 0.003 TYR A 303 PHE 0.021 0.002 PHE B 486 TRP 0.017 0.003 TRP G 63 HIS 0.018 0.002 HIS H 113 Details of bonding type rmsd covalent geometry : bond 0.00466 (17166) covalent geometry : angle 0.76127 (23312) hydrogen bonds : bond 0.04631 ( 866) hydrogen bonds : angle 5.45588 ( 2505) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 152 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 LYS cc_start: 0.8987 (tmtt) cc_final: 0.8579 (tptp) REVERT: A 444 HIS cc_start: 0.8870 (t-170) cc_final: 0.8212 (t-170) REVERT: A 447 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8171 (pm20) REVERT: A 453 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.7501 (t-90) REVERT: E 34 MET cc_start: 0.8432 (ptt) cc_final: 0.7837 (mtt) REVERT: E 155 GLU cc_start: 0.8079 (pt0) cc_final: 0.7052 (pm20) REVERT: F 34 MET cc_start: 0.6772 (tmm) cc_final: 0.6385 (ptp) REVERT: F 51 MET cc_start: 0.5543 (mtt) cc_final: 0.4933 (mtt) REVERT: F 143 PHE cc_start: 0.9089 (m-80) cc_final: 0.8367 (m-80) REVERT: D 92 LEU cc_start: 0.8963 (tp) cc_final: 0.8689 (tp) REVERT: B 439 LYS cc_start: 0.8980 (mmtp) cc_final: 0.8415 (tptp) REVERT: B 447 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8278 (pm20) REVERT: H 34 MET cc_start: 0.6179 (tmm) cc_final: 0.5551 (ptp) REVERT: H 51 MET cc_start: 0.6140 (mtt) cc_final: 0.5568 (mtt) REVERT: H 143 PHE cc_start: 0.9112 (m-80) cc_final: 0.8444 (m-80) REVERT: H 194 ARG cc_start: 0.8381 (tpp-160) cc_final: 0.8102 (tpp-160) REVERT: G 34 MET cc_start: 0.8458 (ptm) cc_final: 0.8110 (mtt) REVERT: G 155 GLU cc_start: 0.7962 (pt0) cc_final: 0.6878 (pm20) outliers start: 55 outliers final: 31 residues processed: 196 average time/residue: 0.1323 time to fit residues: 39.1581 Evaluate side-chains 176 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 447 GLN Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 115 HIS Chi-restraints excluded: chain G residue 171 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 0.9980 chunk 185 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 144 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS F 113 HIS ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN H 113 HIS ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.111668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.088287 restraints weight = 121478.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.088754 restraints weight = 90405.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.089459 restraints weight = 74974.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.089954 restraints weight = 51618.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.091575 restraints weight = 43854.081| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17166 Z= 0.246 Angle : 0.772 10.606 23312 Z= 0.397 Chirality : 0.045 0.209 2720 Planarity : 0.005 0.061 3004 Dihedral : 5.550 40.083 2336 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.35 % Favored : 95.38 % Rotamer: Outliers : 3.18 % Allowed : 16.56 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.17), residues: 2196 helix: 0.27 (0.15), residues: 1056 sheet: -0.16 (0.33), residues: 236 loop : -1.36 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 62 TYR 0.022 0.003 TYR A 303 PHE 0.028 0.002 PHE E 172 TRP 0.016 0.003 TRP G 63 HIS 0.025 0.002 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00518 (17166) covalent geometry : angle 0.77183 (23312) hydrogen bonds : bond 0.04550 ( 866) hydrogen bonds : angle 5.50060 ( 2505) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 147 time to evaluate : 0.762 Fit side-chains REVERT: A 439 LYS cc_start: 0.8978 (tmtt) cc_final: 0.8755 (mmtp) REVERT: A 444 HIS cc_start: 0.8746 (t-170) cc_final: 0.8220 (t-170) REVERT: A 447 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8283 (pm20) REVERT: A 453 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.7369 (t70) REVERT: C 92 LEU cc_start: 0.8807 (tp) cc_final: 0.8555 (tp) REVERT: E 9 ARG cc_start: 0.6942 (ttp80) cc_final: 0.6657 (ttp80) REVERT: E 34 MET cc_start: 0.8188 (ptt) cc_final: 0.7615 (mtt) REVERT: E 155 GLU cc_start: 0.8103 (pt0) cc_final: 0.7068 (pm20) REVERT: F 34 MET cc_start: 0.6541 (tmm) cc_final: 0.6308 (ptp) REVERT: F 51 MET cc_start: 0.5269 (mtt) cc_final: 0.4700 (mtt) REVERT: F 143 PHE cc_start: 0.9081 (m-80) cc_final: 0.8347 (m-80) REVERT: D 92 LEU cc_start: 0.8852 (tp) cc_final: 0.8573 (tp) REVERT: B 439 LYS cc_start: 0.8959 (mmtp) cc_final: 0.8426 (tptp) REVERT: B 447 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8384 (pm20) REVERT: H 34 MET cc_start: 0.5914 (tmm) cc_final: 0.5478 (ptp) REVERT: H 51 MET cc_start: 0.6204 (mtt) cc_final: 0.5880 (mtt) REVERT: H 143 PHE cc_start: 0.9041 (m-80) cc_final: 0.8407 (m-80) REVERT: H 194 ARG cc_start: 0.8368 (tpp-160) cc_final: 0.8124 (tpp-160) REVERT: G 9 ARG cc_start: 0.6899 (ttp80) cc_final: 0.6585 (ttp80) REVERT: G 34 MET cc_start: 0.8186 (ptm) cc_final: 0.7824 (mtt) REVERT: G 155 GLU cc_start: 0.8082 (pt0) cc_final: 0.6849 (pm20) outliers start: 58 outliers final: 37 residues processed: 196 average time/residue: 0.1333 time to fit residues: 38.8031 Evaluate side-chains 180 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 447 GLN Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain H residue 85 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 115 HIS Chi-restraints excluded: chain G residue 171 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 22 optimal weight: 3.9990 chunk 203 optimal weight: 9.9990 chunk 205 optimal weight: 0.3980 chunk 168 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN E 115 HIS F 113 HIS ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 GLN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 HIS ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.112100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.085614 restraints weight = 144965.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.086339 restraints weight = 72879.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.087044 restraints weight = 56999.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.087245 restraints weight = 43348.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.088005 restraints weight = 37723.253| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17166 Z= 0.200 Angle : 0.735 11.463 23312 Z= 0.376 Chirality : 0.044 0.199 2720 Planarity : 0.005 0.058 3004 Dihedral : 5.456 39.433 2336 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.30 % Favored : 95.47 % Rotamer: Outliers : 3.29 % Allowed : 16.89 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.17), residues: 2196 helix: 0.32 (0.15), residues: 1056 sheet: -0.38 (0.33), residues: 236 loop : -1.37 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 158 TYR 0.020 0.002 TYR A 303 PHE 0.032 0.002 PHE G 172 TRP 0.015 0.002 TRP C 290 HIS 0.022 0.002 HIS H 113 Details of bonding type rmsd covalent geometry : bond 0.00427 (17166) covalent geometry : angle 0.73474 (23312) hydrogen bonds : bond 0.04290 ( 866) hydrogen bonds : angle 5.35103 ( 2505) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 154 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 TYR cc_start: 0.6667 (t80) cc_final: 0.6243 (t80) REVERT: A 439 LYS cc_start: 0.9036 (tmtt) cc_final: 0.8608 (tptp) REVERT: A 444 HIS cc_start: 0.8936 (t-170) cc_final: 0.8369 (t-170) REVERT: A 453 HIS cc_start: 0.7759 (OUTLIER) cc_final: 0.7340 (t70) REVERT: C 92 LEU cc_start: 0.8781 (tp) cc_final: 0.8527 (tp) REVERT: E 9 ARG cc_start: 0.6730 (ttp80) cc_final: 0.6319 (ttp80) REVERT: E 34 MET cc_start: 0.8376 (ptt) cc_final: 0.7808 (mtt) REVERT: E 155 GLU cc_start: 0.8063 (pt0) cc_final: 0.7034 (pm20) REVERT: F 34 MET cc_start: 0.6832 (tmm) cc_final: 0.6426 (ptp) REVERT: F 51 MET cc_start: 0.5600 (mtt) cc_final: 0.5176 (mtt) REVERT: F 143 PHE cc_start: 0.9178 (m-80) cc_final: 0.8540 (m-80) REVERT: D 92 LEU cc_start: 0.8925 (tp) cc_final: 0.8644 (tp) REVERT: B 439 LYS cc_start: 0.8974 (mmtp) cc_final: 0.8410 (tptp) REVERT: B 447 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8251 (pm20) REVERT: H 34 MET cc_start: 0.6224 (tmm) cc_final: 0.5583 (ptp) REVERT: H 51 MET cc_start: 0.6455 (mtt) cc_final: 0.6235 (mtt) REVERT: H 72 TYR cc_start: 0.4022 (OUTLIER) cc_final: 0.3555 (p90) REVERT: H 143 PHE cc_start: 0.9169 (m-80) cc_final: 0.8560 (m-80) REVERT: G 9 ARG cc_start: 0.6590 (ttp80) cc_final: 0.6174 (ttp80) REVERT: G 34 MET cc_start: 0.8350 (ptm) cc_final: 0.8092 (mtt) REVERT: G 155 GLU cc_start: 0.7780 (pt0) cc_final: 0.6894 (pm20) outliers start: 59 outliers final: 40 residues processed: 202 average time/residue: 0.1352 time to fit residues: 40.6416 Evaluate side-chains 185 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 447 GLN Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 85 ARG Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 115 HIS Chi-restraints excluded: chain G residue 171 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 159 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 218 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 168 optimal weight: 20.0000 chunk 217 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS F 113 HIS ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 HIS ** H 195 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.112326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.085543 restraints weight = 144040.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.085844 restraints weight = 73961.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.086921 restraints weight = 58215.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.087313 restraints weight = 45564.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.087875 restraints weight = 41025.837| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17166 Z= 0.192 Angle : 0.726 11.780 23312 Z= 0.371 Chirality : 0.044 0.195 2720 Planarity : 0.005 0.057 3004 Dihedral : 5.401 38.757 2336 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.53 % Favored : 95.28 % Rotamer: Outliers : 3.34 % Allowed : 17.49 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.72 (0.17), residues: 2196 helix: 0.33 (0.15), residues: 1056 sheet: -0.54 (0.33), residues: 236 loop : -1.37 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 164 TYR 0.026 0.003 TYR F 146 PHE 0.021 0.002 PHE G 172 TRP 0.014 0.002 TRP C 290 HIS 0.023 0.002 HIS H 113 Details of bonding type rmsd covalent geometry : bond 0.00411 (17166) covalent geometry : angle 0.72646 (23312) hydrogen bonds : bond 0.04231 ( 866) hydrogen bonds : angle 5.30544 ( 2505) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 150 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 LYS cc_start: 0.9061 (tmtt) cc_final: 0.8616 (tptp) REVERT: A 444 HIS cc_start: 0.8980 (t-170) cc_final: 0.8446 (t-170) REVERT: A 453 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.7326 (t70) REVERT: C 92 LEU cc_start: 0.8820 (tp) cc_final: 0.8571 (tp) REVERT: C 260 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7766 (m) REVERT: C 333 MET cc_start: 0.7759 (tpp) cc_final: 0.7553 (tpp) REVERT: E 29 LEU cc_start: 0.7953 (tt) cc_final: 0.7176 (mt) REVERT: E 34 MET cc_start: 0.8338 (ptt) cc_final: 0.7839 (mtt) REVERT: E 155 GLU cc_start: 0.8060 (pt0) cc_final: 0.7004 (pm20) REVERT: F 34 MET cc_start: 0.6880 (tmm) cc_final: 0.6460 (ptp) REVERT: F 51 MET cc_start: 0.5692 (mtt) cc_final: 0.5344 (mtt) REVERT: F 143 PHE cc_start: 0.9211 (m-80) cc_final: 0.8580 (m-80) REVERT: D 92 LEU cc_start: 0.8921 (tp) cc_final: 0.8614 (tp) REVERT: D 260 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7823 (m) REVERT: B 439 LYS cc_start: 0.8967 (mmtp) cc_final: 0.8407 (tptp) REVERT: B 447 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8229 (pm20) REVERT: H 34 MET cc_start: 0.6268 (tmm) cc_final: 0.5602 (ptp) REVERT: H 72 TYR cc_start: 0.4006 (OUTLIER) cc_final: 0.3540 (p90) REVERT: H 143 PHE cc_start: 0.9200 (m-80) cc_final: 0.8614 (m-80) REVERT: G 9 ARG cc_start: 0.6583 (ttp80) cc_final: 0.6191 (ttp80) REVERT: G 34 MET cc_start: 0.8401 (ptm) cc_final: 0.8117 (mtt) REVERT: G 155 GLU cc_start: 0.7966 (pt0) cc_final: 0.6863 (pm20) outliers start: 60 outliers final: 42 residues processed: 200 average time/residue: 0.1291 time to fit residues: 38.9662 Evaluate side-chains 187 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 447 GLN Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 115 HIS Chi-restraints excluded: chain G residue 171 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 180 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 210 optimal weight: 0.4980 chunk 190 optimal weight: 9.9990 chunk 193 optimal weight: 0.1980 chunk 75 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS F 113 HIS ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 GLN H 113 HIS ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.112812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.089255 restraints weight = 129375.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.089997 restraints weight = 91051.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.091184 restraints weight = 70531.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.091518 restraints weight = 50267.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.092290 restraints weight = 43956.439| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17166 Z= 0.165 Angle : 0.712 11.939 23312 Z= 0.361 Chirality : 0.044 0.189 2720 Planarity : 0.005 0.056 3004 Dihedral : 5.329 38.579 2336 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.40 % Favored : 95.42 % Rotamer: Outliers : 2.96 % Allowed : 18.09 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.67 (0.17), residues: 2196 helix: 0.39 (0.15), residues: 1056 sheet: -0.58 (0.33), residues: 236 loop : -1.36 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 158 TYR 0.028 0.002 TYR A 527 PHE 0.029 0.002 PHE E 172 TRP 0.014 0.002 TRP C 290 HIS 0.026 0.002 HIS H 113 Details of bonding type rmsd covalent geometry : bond 0.00358 (17166) covalent geometry : angle 0.71232 (23312) hydrogen bonds : bond 0.04063 ( 866) hydrogen bonds : angle 5.20374 ( 2505) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 150 time to evaluate : 0.625 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: A 439 LYS cc_start: 0.9012 (tmtt) cc_final: 0.8574 (tptp) REVERT: A 444 HIS cc_start: 0.8676 (t-170) cc_final: 0.8288 (t-170) REVERT: A 453 HIS cc_start: 0.7640 (OUTLIER) cc_final: 0.7205 (t70) REVERT: C 260 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7893 (m) REVERT: E 29 LEU cc_start: 0.7883 (tt) cc_final: 0.7097 (mt) REVERT: E 34 MET cc_start: 0.8063 (ptt) cc_final: 0.7537 (mtt) REVERT: E 155 GLU cc_start: 0.7995 (pt0) cc_final: 0.6967 (pm20) REVERT: F 51 MET cc_start: 0.5307 (mtt) cc_final: 0.4916 (mtt) REVERT: F 143 PHE cc_start: 0.9113 (m-80) cc_final: 0.8404 (m-80) REVERT: D 260 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7820 (m) REVERT: D 333 MET cc_start: 0.7492 (tpp) cc_final: 0.7279 (tpp) REVERT: B 439 LYS cc_start: 0.8940 (mmtp) cc_final: 0.8357 (tptp) REVERT: H 34 MET cc_start: 0.5901 (tmm) cc_final: 0.5484 (ptp) REVERT: H 72 TYR cc_start: 0.4221 (OUTLIER) cc_final: 0.3540 (p90) REVERT: H 143 PHE cc_start: 0.9074 (m-80) cc_final: 0.8462 (m-80) REVERT: G 9 ARG cc_start: 0.6549 (ttp80) cc_final: 0.6248 (ttp80) REVERT: G 26 GLN cc_start: 0.7821 (tp-100) cc_final: 0.7494 (tp-100) REVERT: G 34 MET cc_start: 0.8225 (ptm) cc_final: 0.7839 (mtt) REVERT: G 155 GLU cc_start: 0.7964 (pt0) cc_final: 0.6879 (pm20) outliers start: 53 outliers final: 39 residues processed: 194 average time/residue: 0.1315 time to fit residues: 38.5024 Evaluate side-chains 186 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 115 HIS Chi-restraints excluded: chain G residue 171 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 135 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 209 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 202 optimal weight: 20.0000 chunk 146 optimal weight: 0.0050 chunk 78 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS E 115 HIS F 113 HIS ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 GLN B 447 GLN H 113 HIS ** H 195 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.112252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.088800 restraints weight = 133347.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.089857 restraints weight = 95073.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.090785 restraints weight = 72696.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.091334 restraints weight = 51292.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.091884 restraints weight = 44541.158| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3809 r_free = 0.3809 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3809 r_free = 0.3809 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17166 Z= 0.194 Angle : 0.728 11.842 23312 Z= 0.370 Chirality : 0.044 0.195 2720 Planarity : 0.005 0.056 3004 Dihedral : 5.344 38.114 2336 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.62 % Favored : 95.19 % Rotamer: Outliers : 3.34 % Allowed : 17.87 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.74 (0.17), residues: 2196 helix: 0.35 (0.15), residues: 1058 sheet: -0.69 (0.33), residues: 236 loop : -1.39 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 158 TYR 0.028 0.003 TYR B 527 PHE 0.046 0.002 PHE G 172 TRP 0.013 0.002 TRP C 290 HIS 0.027 0.002 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00417 (17166) covalent geometry : angle 0.72766 (23312) hydrogen bonds : bond 0.04107 ( 866) hydrogen bonds : angle 5.22842 ( 2505) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 143 time to evaluate : 0.607 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: A 439 LYS cc_start: 0.9021 (tmtt) cc_final: 0.8752 (mmtp) REVERT: A 444 HIS cc_start: 0.8684 (t-170) cc_final: 0.8297 (t-170) REVERT: A 453 HIS cc_start: 0.7588 (OUTLIER) cc_final: 0.7134 (t70) REVERT: C 260 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.7951 (m) REVERT: E 29 LEU cc_start: 0.7821 (tt) cc_final: 0.7025 (mt) REVERT: E 34 MET cc_start: 0.8069 (ptt) cc_final: 0.7547 (mtt) REVERT: E 155 GLU cc_start: 0.8047 (pt0) cc_final: 0.7039 (pm20) REVERT: F 51 MET cc_start: 0.5404 (mtt) cc_final: 0.4993 (mtt) REVERT: F 143 PHE cc_start: 0.9165 (m-80) cc_final: 0.8496 (m-80) REVERT: D 260 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.7949 (m) REVERT: B 439 LYS cc_start: 0.8943 (mmtp) cc_final: 0.8369 (tptp) REVERT: H 34 MET cc_start: 0.5895 (tmm) cc_final: 0.5488 (ptp) REVERT: H 51 MET cc_start: 0.5818 (mtt) cc_final: 0.2742 (pmm) REVERT: H 72 TYR cc_start: 0.4219 (OUTLIER) cc_final: 0.3530 (p90) REVERT: H 143 PHE cc_start: 0.9122 (m-80) cc_final: 0.8520 (m-80) REVERT: G 9 ARG cc_start: 0.6667 (ttp80) cc_final: 0.6344 (ttp80) REVERT: G 26 GLN cc_start: 0.7841 (tp-100) cc_final: 0.7566 (tp-100) REVERT: G 34 MET cc_start: 0.8229 (ptm) cc_final: 0.7843 (mtt) REVERT: G 155 GLU cc_start: 0.8009 (pt0) cc_final: 0.6913 (pm20) outliers start: 60 outliers final: 50 residues processed: 194 average time/residue: 0.1245 time to fit residues: 36.8586 Evaluate side-chains 195 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 141 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain F residue 86 TYR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 447 GLN Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 115 HIS Chi-restraints excluded: chain G residue 171 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 160 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS F 113 HIS ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 GLN H 113 HIS ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.113545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.090117 restraints weight = 144009.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.092354 restraints weight = 96196.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.092825 restraints weight = 70737.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.093421 restraints weight = 47400.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.095093 restraints weight = 38991.848| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3881 r_free = 0.3881 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3881 r_free = 0.3881 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17166 Z= 0.141 Angle : 0.704 11.773 23312 Z= 0.353 Chirality : 0.044 0.198 2720 Planarity : 0.005 0.056 3004 Dihedral : 5.245 38.341 2336 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.53 % Favored : 95.28 % Rotamer: Outliers : 2.69 % Allowed : 18.48 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.67 (0.18), residues: 2196 helix: 0.42 (0.15), residues: 1060 sheet: -0.64 (0.33), residues: 236 loop : -1.37 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 158 TYR 0.031 0.002 TYR B 527 PHE 0.046 0.002 PHE G 172 TRP 0.014 0.002 TRP C 290 HIS 0.030 0.002 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00307 (17166) covalent geometry : angle 0.70394 (23312) hydrogen bonds : bond 0.03944 ( 866) hydrogen bonds : angle 5.08152 ( 2505) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 0.496 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: A 388 MET cc_start: 0.9203 (tpp) cc_final: 0.8814 (tpp) REVERT: A 439 LYS cc_start: 0.8988 (tmtt) cc_final: 0.8700 (mmtp) REVERT: A 444 HIS cc_start: 0.8593 (t-170) cc_final: 0.8241 (t-170) REVERT: A 453 HIS cc_start: 0.7670 (OUTLIER) cc_final: 0.7242 (t70) REVERT: C 260 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7800 (m) REVERT: E 29 LEU cc_start: 0.7756 (tt) cc_final: 0.6986 (mt) REVERT: E 34 MET cc_start: 0.7995 (ptt) cc_final: 0.7475 (mtt) REVERT: E 155 GLU cc_start: 0.8047 (pt0) cc_final: 0.7037 (pm20) REVERT: F 51 MET cc_start: 0.5323 (mtt) cc_final: 0.4952 (mtt) REVERT: F 143 PHE cc_start: 0.9103 (m-80) cc_final: 0.8452 (m-80) REVERT: D 260 THR cc_start: 0.7981 (OUTLIER) cc_final: 0.7702 (m) REVERT: B 316 GLU cc_start: 0.6963 (tm-30) cc_final: 0.6092 (tm-30) REVERT: B 320 HIS cc_start: 0.7875 (m-70) cc_final: 0.7046 (m-70) REVERT: B 439 LYS cc_start: 0.8943 (mmtp) cc_final: 0.8352 (tptp) REVERT: H 34 MET cc_start: 0.5662 (tmm) cc_final: 0.5353 (ptp) REVERT: H 51 MET cc_start: 0.5709 (mtt) cc_final: 0.2765 (pmm) REVERT: H 143 PHE cc_start: 0.9045 (m-80) cc_final: 0.8513 (m-80) REVERT: G 9 ARG cc_start: 0.6499 (ttp80) cc_final: 0.6258 (ttp80) REVERT: G 26 GLN cc_start: 0.7797 (tp-100) cc_final: 0.7518 (tp-100) REVERT: G 34 MET cc_start: 0.8166 (ptm) cc_final: 0.7752 (mtt) REVERT: G 155 GLU cc_start: 0.7922 (pt0) cc_final: 0.6869 (pm20) outliers start: 48 outliers final: 37 residues processed: 202 average time/residue: 0.1205 time to fit residues: 37.6089 Evaluate side-chains 185 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain G residue 115 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 122 optimal weight: 0.0970 chunk 9 optimal weight: 0.9990 chunk 208 optimal weight: 4.9990 chunk 75 optimal weight: 0.0060 chunk 130 optimal weight: 9.9990 chunk 183 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS E 115 HIS F 113 HIS ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 HIS ** H 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS G 115 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.113869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.090312 restraints weight = 133184.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.091540 restraints weight = 95630.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.093035 restraints weight = 65707.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.092987 restraints weight = 49769.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.094056 restraints weight = 42324.219| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17166 Z= 0.138 Angle : 0.701 11.363 23312 Z= 0.353 Chirality : 0.043 0.172 2720 Planarity : 0.005 0.055 3004 Dihedral : 5.161 38.256 2336 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.58 % Favored : 95.24 % Rotamer: Outliers : 2.52 % Allowed : 19.19 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.18), residues: 2196 helix: 0.43 (0.16), residues: 1058 sheet: -0.57 (0.33), residues: 236 loop : -1.37 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 158 TYR 0.028 0.002 TYR B 527 PHE 0.045 0.002 PHE A 228 TRP 0.014 0.002 TRP C 290 HIS 0.030 0.001 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00301 (17166) covalent geometry : angle 0.70106 (23312) hydrogen bonds : bond 0.03850 ( 866) hydrogen bonds : angle 5.02634 ( 2505) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3006.42 seconds wall clock time: 52 minutes 55.93 seconds (3175.93 seconds total)