Starting phenix.real_space_refine on Fri Mar 6 05:35:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rlo_24535/03_2026/7rlo_24535.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rlo_24535/03_2026/7rlo_24535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rlo_24535/03_2026/7rlo_24535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rlo_24535/03_2026/7rlo_24535.map" model { file = "/net/cci-nas-00/data/ceres_data/7rlo_24535/03_2026/7rlo_24535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rlo_24535/03_2026/7rlo_24535.cif" } resolution = 2.6 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= 0.002 sd= 0.066 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 170 5.16 5 C 18281 2.51 5 N 4997 2.21 5 O 5259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 134 residue(s): 0.03s 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: 28707 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3210 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 395} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3202 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 395} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2604 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 318} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2604 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 318} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2772 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Conformer: "B" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} bond proxies already assigned to first conformer: 2778 Chain: "F" Number of atoms: 2772 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Conformer: "B" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} bond proxies already assigned to first conformer: 2778 Chain: "G" Number of atoms: 2205 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 284, 2194 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 284, 2194 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2218 Chain: "H" Number of atoms: 2205 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 284, 2194 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 284, 2194 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2218 Chain: "I" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1867 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 11, 'TRANS': 226} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "J" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1789 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "K" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1741 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "L" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1736 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 22 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AARG E 321 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 321 " occ=0.50 residue: pdb=" N AARG E 467 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 467 " occ=0.50 residue: pdb=" N AARG F 321 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 321 " occ=0.50 residue: pdb=" N AARG F 467 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 467 " occ=0.50 residue: pdb=" N AARG G 132 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG G 132 " occ=0.50 residue: pdb=" N AARG H 132 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG H 132 " occ=0.50 Time building chain proxies: 7.93, per 1000 atoms: 0.28 Number of scatterers: 28707 At special positions: 0 Unit cell: (131.095, 136.94, 162.825, 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 170 16.00 O 5259 8.00 N 4997 7.00 C 18281 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.2 seconds 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6976 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 35 sheets defined 44.8% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.622A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.688A pdb=" N ILE A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.524A pdb=" N GLU A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 removed outlier: 4.045A pdb=" N CYS A 196 " --> pdb=" O PRO A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 233 removed outlier: 4.221A pdb=" N GLY A 233 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 removed outlier: 4.162A pdb=" N ALA A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 278 removed outlier: 3.897A pdb=" N VAL A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.839A pdb=" N TYR B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 removed outlier: 3.551A pdb=" N ILE B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 142 removed outlier: 3.641A pdb=" N LEU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 175 removed outlier: 3.643A pdb=" N LYS B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 234 removed outlier: 3.654A pdb=" N SER B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.994A pdb=" N ALA B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 260 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 279 removed outlier: 3.670A pdb=" N PHE B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.554A pdb=" N GLN B 333 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER B 334 " --> pdb=" O THR B 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 330 through 334' Processing helix chain 'C' and resid 9 through 25 removed outlier: 3.577A pdb=" N GLY C 25 " --> pdb=" O THR C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 48 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.881A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 98 removed outlier: 4.359A pdb=" N GLY C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 114 Processing helix chain 'C' and resid 128 through 153 removed outlier: 3.797A pdb=" N GLU C 145 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N MET C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 182 Processing helix chain 'C' and resid 199 through 209 removed outlier: 3.617A pdb=" N MET C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 229 removed outlier: 3.591A pdb=" N VAL C 229 " --> pdb=" O MET C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.732A pdb=" N LYS C 273 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 274 " --> pdb=" O MET C 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 270 through 274' Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.695A pdb=" N GLU C 299 " --> pdb=" O PRO C 296 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY C 300 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ILE C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU C 304 " --> pdb=" O ASP C 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 296 through 304' Processing helix chain 'C' and resid 317 through 321 removed outlier: 3.544A pdb=" N LEU C 320 " --> pdb=" O PRO C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 342 removed outlier: 3.585A pdb=" N LEU C 339 " --> pdb=" O TYR C 335 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 341 " --> pdb=" O TYR C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.771A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 25 removed outlier: 3.578A pdb=" N GLY D 25 " --> pdb=" O THR D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 48 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.881A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 98 removed outlier: 4.359A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 128 through 153 removed outlier: 3.798A pdb=" N GLU D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N MET D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLU D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.617A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 229 removed outlier: 3.592A pdb=" N VAL D 229 " --> pdb=" O MET D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.731A pdb=" N LYS D 273 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 274 " --> pdb=" O MET D 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 270 through 274' Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.695A pdb=" N GLU D 299 " --> pdb=" O PRO D 296 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU D 304 " --> pdb=" O ASP D 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 296 through 304' Processing helix chain 'D' and resid 317 through 321 removed outlier: 3.544A pdb=" N LEU D 320 " --> pdb=" O PRO D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 342 removed outlier: 3.585A pdb=" N LEU D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D 341 " --> pdb=" O TYR D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.771A pdb=" N HIS D 349 " --> pdb=" O PRO D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 196 removed outlier: 3.548A pdb=" N MET E 196 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 222 through 239 Processing helix chain 'E' and resid 247 through 267 removed outlier: 3.861A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS E 257 " --> pdb=" O VAL E 253 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 270 through 286 Processing helix chain 'E' and resid 292 through 312 Processing helix chain 'E' and resid 312 through 323 removed outlier: 3.571A pdb=" N GLN E 317 " --> pdb=" O VAL E 313 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE E 319 " --> pdb=" O ALA E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 353 Processing helix chain 'E' and resid 369 through 378 removed outlier: 3.665A pdb=" N SER E 375 " --> pdb=" O HIS E 371 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS E 378 " --> pdb=" O ARG E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 removed outlier: 3.853A pdb=" N VAL E 394 " --> pdb=" O ALA E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 398 No H-bonds generated for 'chain 'E' and resid 396 through 398' Processing helix chain 'E' and resid 420 through 429 removed outlier: 3.542A pdb=" N ALA E 429 " --> pdb=" O LEU E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 443 removed outlier: 3.623A pdb=" N PHE E 443 " --> pdb=" O THR E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 464 removed outlier: 3.600A pdb=" N LEU E 463 " --> pdb=" O PRO E 460 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN E 464 " --> pdb=" O ASP E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 497 Processing helix chain 'E' and resid 511 through 519 Processing helix chain 'F' and resid 192 through 196 Processing helix chain 'F' and resid 204 through 216 Processing helix chain 'F' and resid 221 through 239 Processing helix chain 'F' and resid 247 through 267 removed outlier: 3.986A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS F 257 " --> pdb=" O VAL F 253 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 270 through 286 Processing helix chain 'F' and resid 292 through 312 removed outlier: 3.893A pdb=" N SER F 298 " --> pdb=" O GLU F 294 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE F 312 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 325 removed outlier: 4.064A pdb=" N GLN F 325 " --> pdb=" O AARG F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 353 Processing helix chain 'F' and resid 369 through 379 removed outlier: 3.772A pdb=" N SER F 375 " --> pdb=" O HIS F 371 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA F 379 " --> pdb=" O SER F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 395 removed outlier: 3.563A pdb=" N VAL F 394 " --> pdb=" O ALA F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 398 No H-bonds generated for 'chain 'F' and resid 396 through 398' Processing helix chain 'F' and resid 420 through 429 removed outlier: 3.591A pdb=" N ALA F 429 " --> pdb=" O LEU F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 removed outlier: 3.568A pdb=" N PHE F 443 " --> pdb=" O THR F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 464 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 493 through 497 Processing helix chain 'F' and resid 511 through 519 Processing helix chain 'G' and resid 7 through 15 Processing helix chain 'G' and resid 21 through 36 Processing helix chain 'G' and resid 41 through 60 removed outlier: 3.573A pdb=" N VAL G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 80 removed outlier: 3.869A pdb=" N SER G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 105 Processing helix chain 'G' and resid 106 through 116 removed outlier: 3.637A pdb=" N LEU G 114 " --> pdb=" O LYS G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 119 No H-bonds generated for 'chain 'G' and resid 117 through 119' Processing helix chain 'G' and resid 131 through 143 removed outlier: 3.539A pdb=" N ALA G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 171 Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 182 through 187 Processing helix chain 'G' and resid 188 through 190 No H-bonds generated for 'chain 'G' and resid 188 through 190' Processing helix chain 'G' and resid 212 through 222 Processing helix chain 'G' and resid 247 through 252 removed outlier: 3.592A pdb=" N LYS G 251 " --> pdb=" O PRO G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 295 through 304 Processing helix chain 'H' and resid 6 through 15 removed outlier: 3.555A pdb=" N LYS H 15 " --> pdb=" O LYS H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 36 Processing helix chain 'H' and resid 41 through 60 Processing helix chain 'H' and resid 62 through 81 removed outlier: 3.821A pdb=" N SER H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 105 Processing helix chain 'H' and resid 106 through 116 removed outlier: 3.682A pdb=" N LYS H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 119 No H-bonds generated for 'chain 'H' and resid 117 through 119' Processing helix chain 'H' and resid 131 through 143 Processing helix chain 'H' and resid 159 through 170 removed outlier: 3.905A pdb=" N LYS H 163 " --> pdb=" O LEU H 159 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS H 170 " --> pdb=" O LYS H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 183 removed outlier: 3.776A pdb=" N VAL H 183 " --> pdb=" O ASP H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 221 removed outlier: 3.644A pdb=" N CYS H 218 " --> pdb=" O GLN H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 252 Processing helix chain 'H' and resid 277 through 281 Processing helix chain 'H' and resid 294 through 304 removed outlier: 3.917A pdb=" N ASP H 298 " --> pdb=" O SER H 294 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 28 removed outlier: 3.502A pdb=" N LEU I 27 " --> pdb=" O PRO I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 44 Processing helix chain 'I' and resid 85 through 91 Processing helix chain 'I' and resid 93 through 97 Processing helix chain 'I' and resid 114 through 123 removed outlier: 4.334A pdb=" N LEU I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE I 121 " --> pdb=" O VAL I 117 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA I 123 " --> pdb=" O ASP I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 208 through 218 removed outlier: 4.016A pdb=" N VAL I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 234 removed outlier: 5.005A pdb=" N ILE I 229 " --> pdb=" O ARG I 225 " (cutoff:3.500A) Proline residue: I 230 - end of helix Processing helix chain 'I' and resid 262 through 267 removed outlier: 3.922A pdb=" N PHE I 266 " --> pdb=" O ASP I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 315 through 334 Proline residue: I 327 - end of helix Processing helix chain 'J' and resid 24 through 28 removed outlier: 3.783A pdb=" N LEU J 28 " --> pdb=" O LYS J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 43 Processing helix chain 'J' and resid 86 through 92 removed outlier: 3.527A pdb=" N LEU J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 123 removed outlier: 4.448A pdb=" N LEU J 120 " --> pdb=" O GLU J 116 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE J 121 " --> pdb=" O VAL J 117 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA J 123 " --> pdb=" O ASP J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 190 Processing helix chain 'J' and resid 209 through 218 Processing helix chain 'J' and resid 227 through 234 removed outlier: 3.823A pdb=" N TYR J 231 " --> pdb=" O GLU J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 334 removed outlier: 3.530A pdb=" N TYR J 319 " --> pdb=" O THR J 315 " (cutoff:3.500A) Proline residue: J 327 - end of helix Processing helix chain 'K' and resid 1 through 5 removed outlier: 3.516A pdb=" N TYR K 5 " --> pdb=" O ASN K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 66 Processing helix chain 'K' and resid 90 through 97 Processing helix chain 'K' and resid 101 through 107 removed outlier: 3.514A pdb=" N PHE K 105 " --> pdb=" O ASP K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 117 Processing helix chain 'K' and resid 126 through 132 removed outlier: 4.147A pdb=" N SER K 130 " --> pdb=" O CYS K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 152 Processing helix chain 'K' and resid 158 through 177 Processing helix chain 'K' and resid 180 through 184 Processing helix chain 'K' and resid 188 through 205 Processing helix chain 'K' and resid 206 through 208 No H-bonds generated for 'chain 'K' and resid 206 through 208' Processing helix chain 'K' and resid 218 through 224 Processing helix chain 'L' and resid 1 through 5 removed outlier: 3.594A pdb=" N TYR L 5 " --> pdb=" O ASN L 2 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 66 Processing helix chain 'L' and resid 90 through 97 Processing helix chain 'L' and resid 98 through 100 No H-bonds generated for 'chain 'L' and resid 98 through 100' Processing helix chain 'L' and resid 102 through 107 Processing helix chain 'L' and resid 111 through 117 removed outlier: 3.617A pdb=" N ALA L 116 " --> pdb=" O ASN L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 removed outlier: 3.957A pdb=" N SER L 130 " --> pdb=" O CYS L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 153 removed outlier: 3.644A pdb=" N MET L 153 " --> pdb=" O TYR L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 177 Processing helix chain 'L' and resid 188 through 205 Processing helix chain 'L' and resid 206 through 208 No H-bonds generated for 'chain 'L' and resid 206 through 208' Processing helix chain 'L' and resid 218 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 124 removed outlier: 3.542A pdb=" N CYS A 95 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA A 45 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N PHE A 94 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU A 47 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 151 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR A 152 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N HIS A 248 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS A 247 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE A 184 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE A 249 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR A 182 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AA3, first strand: chain 'A' and resid 212 through 217 removed outlier: 6.283A pdb=" N ALA A 204 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE A 215 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL A 202 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 238 " --> pdb=" O PHE I 195 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP I 161 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU I 167 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 227 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 338 removed outlier: 5.965A pdb=" N LEU A 361 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL A 378 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR A 395 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A 412 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL A 430 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.240A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN A 407 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR A 424 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 384 through 385 removed outlier: 6.239A pdb=" N HIS A 384 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG A 401 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLU A 418 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 119 through 124 removed outlier: 6.599A pdb=" N THR B 91 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE B 123 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL B 93 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA B 45 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N PHE B 94 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU B 47 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 250 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR B 152 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N HIS B 248 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE B 184 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 249 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR B 182 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N MET B 181 " --> pdb=" O HIS B 288 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N HIS B 290 " --> pdb=" O MET B 181 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N MET B 183 " --> pdb=" O HIS B 290 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR B 292 " --> pdb=" O MET B 183 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE B 185 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AB1, first strand: chain 'B' and resid 212 through 217 removed outlier: 6.721A pdb=" N VAL B 212 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASP B 206 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL B 238 " --> pdb=" O PHE J 195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 223 through 226 Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 337 removed outlier: 3.595A pdb=" N ARG B 344 " --> pdb=" O THR B 336 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU B 361 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL B 378 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR B 395 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 412 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL B 430 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 355 through 356 removed outlier: 7.095A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL B 390 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 367 through 368 removed outlier: 6.369A pdb=" N VAL B 367 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N HIS B 384 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG B 401 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLU B 418 " --> pdb=" O VAL B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 423 through 425 removed outlier: 7.163A pdb=" N THR B 424 " --> pdb=" O LEU B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.690A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL C 164 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE C 233 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N MET C 166 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR C 214 " --> pdb=" O ARG F 483 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 239 removed outlier: 3.703A pdb=" N THR C 238 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.109A pdb=" N SER C 307 " --> pdb=" O TYR F 385 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N LEU F 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE F 333 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL F 361 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL F 335 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL F 332 " --> pdb=" O LYS F 400 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU F 402 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LEU F 334 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLY F 404 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N TYR F 336 " --> pdb=" O GLY F 404 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL F 401 " --> pdb=" O LEU F 435 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N CYS F 437 " --> pdb=" O VAL F 401 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU F 403 " --> pdb=" O CYS F 437 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL F 434 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ILE F 501 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL F 436 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 329 through 331 removed outlier: 6.690A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR D 214 " --> pdb=" O ARG E 483 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 239 removed outlier: 3.703A pdb=" N THR D 238 " --> pdb=" O ARG D 246 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 306 through 308 removed outlier: 6.215A pdb=" N SER D 307 " --> pdb=" O TYR E 385 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N LEU E 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE E 333 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL E 361 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL E 335 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR E 336 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLY E 404 " --> pdb=" O TYR E 336 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL E 401 " --> pdb=" O LEU E 435 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N CYS E 437 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU E 403 " --> pdb=" O CYS E 437 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 407 through 408 Processing sheet with id=AC5, first strand: chain 'F' and resid 407 through 408 Processing sheet with id=AC6, first strand: chain 'G' and resid 175 through 178 removed outlier: 8.709A pdb=" N THR G 176 " --> pdb=" O PHE G 148 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL G 150 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL G 178 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL G 152 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL G 193 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL G 229 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL G 195 " --> pdb=" O VAL G 229 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE G 226 " --> pdb=" O LEU G 283 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N PHE G 285 " --> pdb=" O PHE G 226 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL G 228 " --> pdb=" O PHE G 285 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 199 through 200 Processing sheet with id=AC8, first strand: chain 'H' and resid 175 through 178 removed outlier: 6.741A pdb=" N VAL H 150 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL H 178 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL H 152 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N THR H 124 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ILE H 194 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU H 126 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL H 193 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL H 229 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL H 195 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU H 283 " --> pdb=" O PHE H 226 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 199 through 200 Processing sheet with id=AD1, first strand: chain 'I' and resid 73 through 77 removed outlier: 4.039A pdb=" N MET I 8 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER I 105 " --> pdb=" O HIS I 203 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N HIS I 203 " --> pdb=" O SER I 105 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU I 131 " --> pdb=" O ALA I 202 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU I 204 " --> pdb=" O ALA I 129 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA I 129 " --> pdb=" O LEU I 204 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 51 through 54 removed outlier: 9.115A pdb=" N ILE J 52 " --> pdb=" O PHE J 3 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA J 5 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL J 54 " --> pdb=" O ALA J 5 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL J 7 " --> pdb=" O VAL J 54 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER J 105 " --> pdb=" O HIS J 203 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N HIS J 203 " --> pdb=" O SER J 105 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ALA J 202 " --> pdb=" O ARG J 133 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N ARG J 133 " --> pdb=" O ALA J 202 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU J 204 " --> pdb=" O LEU J 131 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 8 through 13 removed outlier: 3.548A pdb=" N SER K 26 " --> pdb=" O ALA K 11 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 37 through 40 removed outlier: 4.452A pdb=" N ASP K 37 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 52 through 54 Processing sheet with id=AD6, first strand: chain 'L' and resid 8 through 13 removed outlier: 3.846A pdb=" N SER L 26 " --> pdb=" O ALA L 11 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN L 13 " --> pdb=" O SER L 24 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER L 24 " --> pdb=" O ASN L 13 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 37 through 40 removed outlier: 4.461A pdb=" N ASP L 37 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 52 through 54 1171 hydrogen bonds defined for protein. 3317 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: 4.89 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9455 1.34 - 1.46: 5715 1.46 - 1.58: 13829 1.58 - 1.69: 0 1.69 - 1.81: 258 Bond restraints: 29257 Sorted by residual: bond pdb=" C LYS I 25 " pdb=" N PRO I 26 " ideal model delta sigma weight residual 1.336 1.361 -0.025 1.08e-02 8.57e+03 5.53e+00 bond pdb=" C VAL I 326 " pdb=" N PRO I 327 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.24e+00 bond pdb=" C LEU F 395 " pdb=" N PRO F 396 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.19e-02 7.06e+03 3.20e+00 bond pdb=" C VAL J 326 " pdb=" N PRO J 327 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.99e+00 bond pdb=" CA ILE L 14 " pdb=" CB ILE L 14 " ideal model delta sigma weight residual 1.528 1.546 -0.019 1.34e-02 5.57e+03 1.91e+00 ... (remaining 29252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 39167 1.70 - 3.40: 392 3.40 - 5.11: 65 5.11 - 6.81: 20 6.81 - 8.51: 5 Bond angle restraints: 39649 Sorted by residual: angle pdb=" N ARG K 17 " pdb=" CA ARG K 17 " pdb=" C ARG K 17 " ideal model delta sigma weight residual 113.18 106.06 7.12 1.33e+00 5.65e-01 2.87e+01 angle pdb=" C VAL J 76 " pdb=" N CYS J 77 " pdb=" CA CYS J 77 " ideal model delta sigma weight residual 121.56 128.99 -7.43 1.56e+00 4.11e-01 2.27e+01 angle pdb=" N ARG L 17 " pdb=" CA ARG L 17 " pdb=" C ARG L 17 " ideal model delta sigma weight residual 112.72 107.20 5.52 1.28e+00 6.10e-01 1.86e+01 angle pdb=" N CYS J 77 " pdb=" CA CYS J 77 " pdb=" C CYS J 77 " ideal model delta sigma weight residual 110.42 116.59 -6.17 1.46e+00 4.69e-01 1.78e+01 angle pdb=" N VAL J 326 " pdb=" CA VAL J 326 " pdb=" C VAL J 326 " ideal model delta sigma weight residual 108.88 117.30 -8.42 2.16e+00 2.14e-01 1.52e+01 ... (remaining 39644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 16246 17.94 - 35.88: 1106 35.88 - 53.81: 316 53.81 - 71.75: 59 71.75 - 89.69: 33 Dihedral angle restraints: 17760 sinusoidal: 7018 harmonic: 10742 Sorted by residual: dihedral pdb=" CA VAL K 16 " pdb=" C VAL K 16 " pdb=" N ARG K 17 " pdb=" CA ARG K 17 " ideal model delta harmonic sigma weight residual 180.00 152.84 27.16 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA VAL L 16 " pdb=" C VAL L 16 " pdb=" N ARG L 17 " pdb=" CA ARG L 17 " ideal model delta harmonic sigma weight residual 180.00 154.74 25.26 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA PRO A 453 " pdb=" C PRO A 453 " pdb=" N PRO A 454 " pdb=" CA PRO A 454 " ideal model delta harmonic sigma weight residual 180.00 -157.39 -22.61 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 17757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3156 0.034 - 0.069: 984 0.069 - 0.103: 335 0.103 - 0.138: 150 0.138 - 0.172: 3 Chirality restraints: 4628 Sorted by residual: chirality pdb=" CG LEU K 201 " pdb=" CB LEU K 201 " pdb=" CD1 LEU K 201 " pdb=" CD2 LEU K 201 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CA PRO I 327 " pdb=" N PRO I 327 " pdb=" C PRO I 327 " pdb=" CB PRO I 327 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA VAL J 46 " pdb=" N VAL J 46 " pdb=" C VAL J 46 " pdb=" CB VAL J 46 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 4625 not shown) Planarity restraints: 5049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 395 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO E 396 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO E 396 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 396 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 395 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO F 396 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO F 396 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 396 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 326 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.03e+00 pdb=" C VAL J 326 " 0.025 2.00e-02 2.50e+03 pdb=" O VAL J 326 " -0.009 2.00e-02 2.50e+03 pdb=" N PRO J 327 " -0.008 2.00e-02 2.50e+03 ... (remaining 5046 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 583 2.69 - 3.24: 26830 3.24 - 3.79: 44153 3.79 - 4.35: 60674 4.35 - 4.90: 100723 Nonbonded interactions: 232963 Sorted by model distance: nonbonded pdb=" OD2 ASP G 85 " pdb=" OG SER G 87 " model vdw 2.132 3.040 nonbonded pdb=" OD1 ASP C 121 " pdb=" OG SER C 123 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASP D 121 " pdb=" OG SER D 123 " model vdw 2.200 3.040 nonbonded pdb=" O SER G 80 " pdb=" OG SER G 80 " model vdw 2.250 3.040 nonbonded pdb=" OE1 GLU A 198 " pdb=" NE2 GLN A 219 " model vdw 2.273 3.120 ... (remaining 232958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 41 through 433 or (resid 434 and (name N or name CA or nam \ e C or name O or name CB )) or resid 435 through 456 or (resid 457 and (name N o \ r name CA or name C or name O or name CB )) or resid 458 through 459)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 167 through 320 or resid 322 through 466 or resid 468 thro \ ugh 519)) selection = (chain 'F' and (resid 167 through 320 or resid 322 through 466 or resid 468 thro \ ugh 519)) } ncs_group { reference = (chain 'G' and (resid 5 through 131 or resid 133 through 305)) selection = (chain 'H' and (resid 5 through 131 or resid 133 through 305)) } ncs_group { reference = (chain 'I' and (resid 1 through 78 or resid 84 through 235 or resid 297 through \ 334)) selection = (chain 'J' and (resid 1 through 77 or (resid 78 and (name N or name CA or name C \ or name O or name CB )) or resid 84 through 334)) } ncs_group { reference = (chain 'K' and (resid 1 through 220 or (resid 221 through 226 and (name N or nam \ e CA or name C or name O or name CB )))) selection = chain 'L' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.720 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 0.002 0.047 29257 Z= 0.101 Angle : 0.489 8.511 39649 Z= 0.282 Chirality : 0.041 0.172 4628 Planarity : 0.003 0.039 5049 Dihedral : 14.087 89.691 10784 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.36 % Favored : 95.59 % Rotamer: Outliers : 3.01 % Allowed : 15.77 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.13), residues: 3622 helix: -0.59 (0.13), residues: 1409 sheet: -1.62 (0.23), residues: 474 loop : -1.95 (0.13), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 17 TYR 0.015 0.001 TYR L 65 PHE 0.010 0.001 PHE C 177 TRP 0.003 0.000 TRP A 111 HIS 0.002 0.000 HIS L 19 Details of bonding type rmsd covalent geometry : bond 0.00196 (29257) covalent geometry : angle 0.48881 (39649) hydrogen bonds : bond 0.16556 ( 1171) hydrogen bonds : angle 6.00701 ( 3317) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 405 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 HIS cc_start: 0.5289 (m-70) cc_final: 0.5044 (m-70) REVERT: B 145 ARG cc_start: 0.8047 (mtm180) cc_final: 0.7842 (mtm180) REVERT: B 348 VAL cc_start: 0.6801 (OUTLIER) cc_final: 0.6354 (t) REVERT: B 357 GLU cc_start: 0.7818 (tt0) cc_final: 0.7510 (tt0) REVERT: C 9 SER cc_start: 0.6949 (OUTLIER) cc_final: 0.5823 (t) REVERT: C 13 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7692 (mp0) REVERT: C 20 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8056 (mm-30) REVERT: C 48 ASP cc_start: 0.7941 (m-30) cc_final: 0.7468 (m-30) REVERT: C 115 SER cc_start: 0.7961 (OUTLIER) cc_final: 0.7696 (p) REVERT: C 226 MET cc_start: 0.8686 (tpt) cc_final: 0.8346 (tpp) REVERT: D 21 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8893 (t) REVERT: D 350 VAL cc_start: 0.9162 (p) cc_final: 0.8919 (t) REVERT: F 415 MET cc_start: 0.8230 (ttp) cc_final: 0.7746 (ttm) REVERT: F 462 ASP cc_start: 0.8184 (m-30) cc_final: 0.7924 (m-30) REVERT: H 13 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8306 (pp30) REVERT: I 71 MET cc_start: 0.6683 (ttm) cc_final: 0.6451 (ttp) REVERT: J 50 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6873 (tm-30) REVERT: J 214 PHE cc_start: 0.8164 (t80) cc_final: 0.7831 (t80) REVERT: K 93 MET cc_start: 0.8451 (tmm) cc_final: 0.7340 (tpp) REVERT: K 110 LEU cc_start: 0.3846 (OUTLIER) cc_final: 0.3241 (mm) REVERT: K 127 GLU cc_start: 0.7286 (pt0) cc_final: 0.7039 (pt0) REVERT: L 115 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8350 (ttpt) REVERT: L 182 GLU cc_start: 0.7938 (pp20) cc_final: 0.7491 (pp20) REVERT: L 183 HIS cc_start: 0.8618 (m-70) cc_final: 0.7869 (m90) outliers start: 94 outliers final: 32 residues processed: 487 average time/residue: 0.7345 time to fit residues: 410.3298 Evaluate side-chains 288 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 249 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain I residue 25 LYS Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 14 ILE Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain L residue 115 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.0170 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.3980 overall best weight: 1.4822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 89 GLN A 160 ASN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 GLN A 359 ASN A 376 ASN B 44 GLN B 72 ASN B 219 GLN B 290 HIS B 337 HIS B 359 ASN B 393 GLN B 398 GLN B 416 ASN C 80 ASN C 125 HIS C 130 GLN C 158 HIS C 160 HIS C 277 GLN D 80 ASN D 125 HIS D 130 GLN D 158 HIS D 160 HIS D 230 ASN E 194 GLN E 213 GLN E 235 GLN E 281 ASN E 325 GLN E 422 GLN E 430 HIS E 448 GLN E 464 GLN F 213 GLN F 281 ASN F 371 HIS F 430 HIS F 448 GLN F 455 ASN F 464 GLN F 470 HIS G 109 ASN G 243 GLN G 244 GLN H 109 ASN H 222 GLN H 243 GLN I 218 ASN I 297 GLN I 323 ASN I 325 GLN J 32 ASN J 136 GLN J 190 HIS J 218 ASN J 325 GLN K 19 HIS K 59 ASN K 112 ASN K 145 GLN L 13 ASN L 34 HIS L 91 GLN L 112 ASN L 145 GLN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.113397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.077231 restraints weight = 116349.004| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.64 r_work: 0.2932 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 29257 Z= 0.156 Angle : 0.577 11.345 39649 Z= 0.294 Chirality : 0.045 0.250 4628 Planarity : 0.004 0.048 5049 Dihedral : 5.325 59.698 4046 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.64 % Allowed : 17.93 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3622 helix: 0.66 (0.14), residues: 1459 sheet: -0.98 (0.25), residues: 449 loop : -1.35 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 102 TYR 0.025 0.002 TYR K 65 PHE 0.022 0.001 PHE D 177 TRP 0.007 0.001 TRP E 350 HIS 0.011 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00378 (29257) covalent geometry : angle 0.57692 (39649) hydrogen bonds : bond 0.03735 ( 1171) hydrogen bonds : angle 4.23859 ( 3317) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 261 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 HIS cc_start: 0.7928 (t-90) cc_final: 0.7669 (t-90) REVERT: B 145 ARG cc_start: 0.8474 (mtm180) cc_final: 0.8187 (mtm180) REVERT: B 349 SER cc_start: 0.6449 (OUTLIER) cc_final: 0.6233 (p) REVERT: B 357 GLU cc_start: 0.8300 (tt0) cc_final: 0.7788 (tt0) REVERT: C 20 GLU cc_start: 0.8564 (tp30) cc_final: 0.8142 (mm-30) REVERT: C 226 MET cc_start: 0.8862 (tpt) cc_final: 0.8458 (tpp) REVERT: D 21 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8686 (t) REVERT: D 305 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8621 (mtpp) REVERT: F 415 MET cc_start: 0.8986 (ttp) cc_final: 0.8660 (ttm) REVERT: F 455 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8442 (t0) REVERT: G 8 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: H 13 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8800 (pp30) REVERT: H 139 GLU cc_start: 0.8091 (tt0) cc_final: 0.7778 (mt-10) REVERT: J 216 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7033 (ttm) REVERT: J 217 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8247 (tm-30) REVERT: J 305 MET cc_start: 0.6024 (OUTLIER) cc_final: 0.5785 (mtm) REVERT: J 318 LEU cc_start: 0.8194 (pt) cc_final: 0.7796 (tt) REVERT: K 93 MET cc_start: 0.8719 (tmm) cc_final: 0.7605 (mpp) REVERT: L 175 ARG cc_start: 0.8445 (mpp80) cc_final: 0.8178 (mpp80) REVERT: L 182 GLU cc_start: 0.7857 (pp20) cc_final: 0.7603 (pp20) outliers start: 114 outliers final: 41 residues processed: 347 average time/residue: 0.7189 time to fit residues: 288.8613 Evaluate side-chains 280 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 519 LYS Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 455 ASN Chi-restraints excluded: chain F residue 470 HIS Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 25 LYS Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 217 GLU Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 305 MET Chi-restraints excluded: chain K residue 14 ILE Chi-restraints excluded: chain K residue 183 HIS Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 133 SER Chi-restraints excluded: chain L residue 198 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 194 optimal weight: 2.9990 chunk 309 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 329 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 chunk 359 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 300 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN C 277 GLN E 431 ASN F 422 GLN G 244 GLN I 41 ASN J 325 GLN L 36 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.109119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.071941 restraints weight = 104910.427| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.52 r_work: 0.2843 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 29257 Z= 0.240 Angle : 0.641 9.758 39649 Z= 0.327 Chirality : 0.048 0.177 4628 Planarity : 0.005 0.053 5049 Dihedral : 5.152 58.028 4011 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.88 % Favored : 95.06 % Rotamer: Outliers : 3.99 % Allowed : 17.36 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.36 (0.14), residues: 3622 helix: 0.96 (0.14), residues: 1475 sheet: -0.88 (0.24), residues: 467 loop : -1.10 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 225 TYR 0.026 0.002 TYR G 86 PHE 0.023 0.002 PHE D 177 TRP 0.009 0.002 TRP K 74 HIS 0.057 0.002 HIS F 470 Details of bonding type rmsd covalent geometry : bond 0.00593 (29257) covalent geometry : angle 0.64069 (39649) hydrogen bonds : bond 0.04592 ( 1171) hydrogen bonds : angle 4.28599 ( 3317) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 243 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: A 359 ASN cc_start: 0.9121 (OUTLIER) cc_final: 0.8884 (m110) REVERT: B 127 LEU cc_start: 0.8403 (mt) cc_final: 0.7798 (pt) REVERT: B 145 ARG cc_start: 0.8537 (mtm180) cc_final: 0.8251 (mtm180) REVERT: B 349 SER cc_start: 0.7026 (OUTLIER) cc_final: 0.6800 (p) REVERT: B 355 ILE cc_start: 0.8346 (mt) cc_final: 0.8049 (mm) REVERT: C 24 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7614 (mtp180) REVERT: C 149 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8010 (tm-30) REVERT: C 226 MET cc_start: 0.8918 (tpt) cc_final: 0.8651 (tpp) REVERT: D 31 SER cc_start: 0.8076 (OUTLIER) cc_final: 0.7790 (p) REVERT: D 186 LYS cc_start: 0.9024 (tttp) cc_final: 0.8604 (ttmm) REVERT: D 305 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8645 (mtpp) REVERT: E 292 ARG cc_start: 0.6755 (ttm-80) cc_final: 0.6508 (ttm-80) REVERT: E 445 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8414 (mt-10) REVERT: G 13 GLN cc_start: 0.8876 (pp30) cc_final: 0.8543 (pp30) REVERT: H 13 GLN cc_start: 0.8935 (tm-30) cc_final: 0.8417 (pp30) REVERT: H 14 MET cc_start: 0.8636 (mmp) cc_final: 0.8340 (tpp) REVERT: I 218 ASN cc_start: 0.7136 (m-40) cc_final: 0.6860 (m110) REVERT: J 170 MET cc_start: 0.5762 (OUTLIER) cc_final: 0.5415 (ttt) REVERT: J 216 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6992 (ttm) REVERT: J 217 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8300 (tm-30) REVERT: J 318 LEU cc_start: 0.8100 (pt) cc_final: 0.7741 (tt) REVERT: K 59 ASN cc_start: 0.8399 (t0) cc_final: 0.8078 (m-40) REVERT: K 93 MET cc_start: 0.8914 (tmm) cc_final: 0.7575 (mpp) REVERT: K 141 GLN cc_start: 0.8547 (mp10) cc_final: 0.8289 (mp10) REVERT: K 218 VAL cc_start: 0.7718 (OUTLIER) cc_final: 0.7409 (t) REVERT: L 173 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: L 175 ARG cc_start: 0.8472 (mpp80) cc_final: 0.8262 (mpp80) REVERT: L 182 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7344 (pp20) REVERT: L 183 HIS cc_start: 0.8730 (m-70) cc_final: 0.8019 (m90) outliers start: 125 outliers final: 53 residues processed: 347 average time/residue: 0.6695 time to fit residues: 270.4044 Evaluate side-chains 293 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 227 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain E residue 519 LYS Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 25 LYS Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 162 SER Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 217 GLU Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 311 SER Chi-restraints excluded: chain K residue 14 ILE Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 133 SER Chi-restraints excluded: chain L residue 173 GLU Chi-restraints excluded: chain L residue 182 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 55 optimal weight: 2.9990 chunk 270 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 343 optimal weight: 5.9990 chunk 262 optimal weight: 0.0010 chunk 278 optimal weight: 9.9990 chunk 350 optimal weight: 0.0980 chunk 263 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 315 optimal weight: 4.9990 chunk 226 optimal weight: 4.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN C 277 GLN D 44 GLN L 59 ASN L 145 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.111317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.073992 restraints weight = 116451.019| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.99 r_work: 0.2864 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29257 Z= 0.131 Angle : 0.543 8.606 39649 Z= 0.278 Chirality : 0.044 0.165 4628 Planarity : 0.004 0.055 5049 Dihedral : 4.764 58.267 4007 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.29 % Allowed : 18.25 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 3622 helix: 1.31 (0.14), residues: 1465 sheet: -0.55 (0.26), residues: 444 loop : -0.91 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 95 TYR 0.018 0.001 TYR G 86 PHE 0.016 0.001 PHE D 177 TRP 0.009 0.001 TRP A 111 HIS 0.007 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00317 (29257) covalent geometry : angle 0.54304 (39649) hydrogen bonds : bond 0.03459 ( 1171) hydrogen bonds : angle 4.03339 ( 3317) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 244 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 ASN cc_start: 0.8942 (OUTLIER) cc_final: 0.8728 (m110) REVERT: B 127 LEU cc_start: 0.8448 (mt) cc_final: 0.7803 (pt) REVERT: B 145 ARG cc_start: 0.8501 (mtm180) cc_final: 0.8203 (mtm180) REVERT: B 289 MET cc_start: 0.8104 (ttp) cc_final: 0.7849 (ttp) REVERT: B 355 ILE cc_start: 0.8315 (mt) cc_final: 0.8022 (mm) REVERT: C 44 GLN cc_start: 0.8559 (tp40) cc_final: 0.8283 (tp40) REVERT: C 48 ASP cc_start: 0.8185 (m-30) cc_final: 0.7946 (m-30) REVERT: C 226 MET cc_start: 0.8894 (tpt) cc_final: 0.8609 (tpp) REVERT: E 445 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8412 (mt-10) REVERT: F 247 GLU cc_start: 0.6510 (pm20) cc_final: 0.6228 (pm20) REVERT: F 328 SER cc_start: 0.9023 (OUTLIER) cc_final: 0.8523 (p) REVERT: F 495 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8651 (pm20) REVERT: G 13 GLN cc_start: 0.8837 (pp30) cc_final: 0.8399 (pp30) REVERT: G 33 PHE cc_start: 0.8247 (m-80) cc_final: 0.8007 (m-80) REVERT: G 103 ARG cc_start: 0.8308 (ttm110) cc_final: 0.7482 (tpt90) REVERT: G 180 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8697 (m-30) REVERT: H 13 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8375 (pp30) REVERT: H 14 MET cc_start: 0.8612 (mmp) cc_final: 0.8267 (tpp) REVERT: I 38 TYR cc_start: 0.7409 (m-80) cc_final: 0.7146 (m-80) REVERT: I 218 ASN cc_start: 0.7281 (m-40) cc_final: 0.7053 (m110) REVERT: J 72 LYS cc_start: 0.7919 (tppt) cc_final: 0.7351 (ttpp) REVERT: J 170 MET cc_start: 0.5620 (OUTLIER) cc_final: 0.5288 (ttt) REVERT: J 209 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7055 (mmtp) REVERT: J 216 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6692 (mtp) REVERT: J 305 MET cc_start: 0.6225 (OUTLIER) cc_final: 0.5860 (mtp) REVERT: J 318 LEU cc_start: 0.8107 (pt) cc_final: 0.7732 (tt) REVERT: K 59 ASN cc_start: 0.8427 (t0) cc_final: 0.8002 (m110) REVERT: K 93 MET cc_start: 0.8918 (tmm) cc_final: 0.7602 (mpp) REVERT: K 218 VAL cc_start: 0.7848 (OUTLIER) cc_final: 0.7570 (t) REVERT: L 1 MET cc_start: 0.7127 (tpp) cc_final: 0.6033 (tpp) REVERT: L 33 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7017 (t80) REVERT: L 173 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: L 175 ARG cc_start: 0.8444 (mpp80) cc_final: 0.8224 (mpp80) REVERT: L 182 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7308 (pp20) REVERT: L 183 HIS cc_start: 0.8750 (m-70) cc_final: 0.8035 (m90) outliers start: 103 outliers final: 48 residues processed: 328 average time/residue: 0.6779 time to fit residues: 259.7367 Evaluate side-chains 295 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 234 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 25 LYS Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain I residue 297 GLN Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 162 SER Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 209 LYS Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 305 MET Chi-restraints excluded: chain K residue 14 ILE Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 183 HIS Chi-restraints excluded: chain K residue 208 ASP Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain L residue 33 PHE Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 133 SER Chi-restraints excluded: chain L residue 173 GLU Chi-restraints excluded: chain L residue 182 GLU Chi-restraints excluded: chain L residue 198 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 257 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 319 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 321 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 312 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 313 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN C 277 GLN D 44 GLN F 470 HIS J 218 ASN L 165 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.107784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.071020 restraints weight = 126888.173| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.74 r_work: 0.2816 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 29257 Z= 0.255 Angle : 0.639 11.389 39649 Z= 0.326 Chirality : 0.048 0.184 4628 Planarity : 0.004 0.057 5049 Dihedral : 5.076 57.271 4004 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.97 % Favored : 94.98 % Rotamer: Outliers : 3.96 % Allowed : 17.93 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.02 (0.14), residues: 3622 helix: 1.21 (0.14), residues: 1475 sheet: -0.66 (0.25), residues: 468 loop : -0.90 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 222 TYR 0.024 0.002 TYR G 86 PHE 0.020 0.002 PHE D 177 TRP 0.011 0.001 TRP A 111 HIS 0.008 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00632 (29257) covalent geometry : angle 0.63857 (39649) hydrogen bonds : bond 0.04465 ( 1171) hydrogen bonds : angle 4.20351 ( 3317) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 242 time to evaluate : 1.129 Fit side-chains REVERT: A 359 ASN cc_start: 0.9065 (OUTLIER) cc_final: 0.8692 (m110) REVERT: B 127 LEU cc_start: 0.8559 (mt) cc_final: 0.7927 (pt) REVERT: B 145 ARG cc_start: 0.8536 (mtm180) cc_final: 0.8217 (mtm180) REVERT: B 355 ILE cc_start: 0.8273 (mt) cc_final: 0.7998 (mm) REVERT: C 24 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7689 (mtp180) REVERT: C 226 MET cc_start: 0.8943 (tpt) cc_final: 0.8655 (tpp) REVERT: D 139 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8014 (mt-10) REVERT: D 186 LYS cc_start: 0.9016 (tttp) cc_final: 0.8622 (ttmm) REVERT: E 445 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8449 (mt-10) REVERT: F 247 GLU cc_start: 0.6757 (pm20) cc_final: 0.6469 (pm20) REVERT: G 13 GLN cc_start: 0.8920 (pp30) cc_final: 0.8516 (pp30) REVERT: G 103 ARG cc_start: 0.8387 (ttm110) cc_final: 0.7583 (tpt90) REVERT: I 38 TYR cc_start: 0.7478 (m-80) cc_final: 0.7244 (m-80) REVERT: I 218 ASN cc_start: 0.7352 (m-40) cc_final: 0.7128 (m110) REVERT: J 72 LYS cc_start: 0.7805 (tppt) cc_final: 0.7477 (ttpp) REVERT: J 170 MET cc_start: 0.5692 (OUTLIER) cc_final: 0.5347 (ttt) REVERT: J 209 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7149 (mmtp) REVERT: J 216 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.6850 (tpt) REVERT: K 93 MET cc_start: 0.8955 (tmm) cc_final: 0.7550 (mpp) REVERT: K 141 GLN cc_start: 0.8533 (mp10) cc_final: 0.8301 (mp10) REVERT: K 182 GLU cc_start: 0.8318 (pp20) cc_final: 0.8111 (pm20) REVERT: K 218 VAL cc_start: 0.7930 (OUTLIER) cc_final: 0.7649 (t) REVERT: L 175 ARG cc_start: 0.8432 (mpp80) cc_final: 0.8206 (mpp80) REVERT: L 182 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7316 (pp20) REVERT: L 183 HIS cc_start: 0.8798 (m-70) cc_final: 0.8083 (m90) outliers start: 124 outliers final: 69 residues processed: 345 average time/residue: 0.6973 time to fit residues: 279.6565 Evaluate side-chains 313 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 236 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 470 HIS Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 239 PHE Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 25 LYS Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain I residue 297 GLN Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 311 SER Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 162 SER Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 209 LYS Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 311 SER Chi-restraints excluded: chain K residue 14 ILE Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 183 HIS Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 133 SER Chi-restraints excluded: chain L residue 182 GLU Chi-restraints excluded: chain L residue 195 SER Chi-restraints excluded: chain L residue 198 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 154 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 278 optimal weight: 8.9990 chunk 219 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 chunk 313 optimal weight: 1.9990 chunk 304 optimal weight: 0.4980 chunk 217 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS A 409 HIS ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN C 277 GLN D 44 GLN F 470 HIS J 218 ASN L 59 ASN L 145 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.111656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.074772 restraints weight = 136619.783| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 4.26 r_work: 0.2868 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29257 Z= 0.107 Angle : 0.539 9.739 39649 Z= 0.275 Chirality : 0.044 0.163 4628 Planarity : 0.004 0.056 5049 Dihedral : 4.659 57.922 4004 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.82 % Allowed : 19.04 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3622 helix: 1.57 (0.14), residues: 1464 sheet: -0.36 (0.26), residues: 434 loop : -0.74 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 292 TYR 0.016 0.001 TYR L 65 PHE 0.014 0.001 PHE C 177 TRP 0.015 0.001 TRP L 119 HIS 0.021 0.001 HIS F 470 Details of bonding type rmsd covalent geometry : bond 0.00249 (29257) covalent geometry : angle 0.53897 (39649) hydrogen bonds : bond 0.03130 ( 1171) hydrogen bonds : angle 3.90720 ( 3317) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 251 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.8528 (mt) cc_final: 0.7882 (pt) REVERT: B 145 ARG cc_start: 0.8522 (mtm180) cc_final: 0.8207 (mtm180) REVERT: B 355 ILE cc_start: 0.8324 (mt) cc_final: 0.8045 (mm) REVERT: C 226 MET cc_start: 0.8906 (tpt) cc_final: 0.8616 (tpp) REVERT: D 139 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8009 (mt-10) REVERT: E 445 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8415 (mt-10) REVERT: F 247 GLU cc_start: 0.6484 (pm20) cc_final: 0.6219 (pm20) REVERT: F 328 SER cc_start: 0.8999 (OUTLIER) cc_final: 0.8528 (p) REVERT: G 13 GLN cc_start: 0.8851 (pp30) cc_final: 0.8401 (pp30) REVERT: G 103 ARG cc_start: 0.8361 (ttm110) cc_final: 0.7543 (tpt90) REVERT: H 13 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8417 (pp30) REVERT: I 218 ASN cc_start: 0.7344 (m-40) cc_final: 0.7121 (m110) REVERT: J 1 MET cc_start: 0.7928 (mtp) cc_final: 0.7508 (mmt) REVERT: J 170 MET cc_start: 0.5509 (OUTLIER) cc_final: 0.5219 (ttt) REVERT: J 216 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6717 (mmm) REVERT: J 318 LEU cc_start: 0.8312 (pt) cc_final: 0.7865 (tt) REVERT: K 59 ASN cc_start: 0.8513 (t0) cc_final: 0.8157 (m-40) REVERT: K 86 MET cc_start: 0.7216 (ttm) cc_final: 0.6989 (ttp) REVERT: K 93 MET cc_start: 0.8877 (tmm) cc_final: 0.7573 (mpp) REVERT: L 1 MET cc_start: 0.7134 (tpp) cc_final: 0.5929 (tpp) REVERT: L 33 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.6900 (t80) REVERT: L 135 ARG cc_start: 0.7825 (tmm160) cc_final: 0.7599 (tmm160) REVERT: L 182 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7226 (pp20) REVERT: L 183 HIS cc_start: 0.8782 (m-70) cc_final: 0.8053 (m90) outliers start: 88 outliers final: 44 residues processed: 324 average time/residue: 0.6400 time to fit residues: 241.7480 Evaluate side-chains 285 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 235 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 25 LYS Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain I residue 297 GLN Chi-restraints excluded: chain I residue 311 SER Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 311 SER Chi-restraints excluded: chain K residue 14 ILE Chi-restraints excluded: chain K residue 183 HIS Chi-restraints excluded: chain L residue 33 PHE Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 133 SER Chi-restraints excluded: chain L residue 182 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 258 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 285 optimal weight: 0.0970 chunk 92 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN C 277 GLN D 44 GLN F 470 HIS J 218 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.109898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.073321 restraints weight = 133336.059| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.82 r_work: 0.2854 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29257 Z= 0.151 Angle : 0.569 10.440 39649 Z= 0.289 Chirality : 0.045 0.164 4628 Planarity : 0.004 0.056 5049 Dihedral : 4.711 57.659 4003 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.82 % Allowed : 19.20 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3622 helix: 1.61 (0.14), residues: 1464 sheet: -0.38 (0.25), residues: 460 loop : -0.69 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 292 TYR 0.020 0.001 TYR J 231 PHE 0.016 0.001 PHE D 177 TRP 0.021 0.001 TRP L 119 HIS 0.008 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00371 (29257) covalent geometry : angle 0.56924 (39649) hydrogen bonds : bond 0.03551 ( 1171) hydrogen bonds : angle 3.92792 ( 3317) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 244 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.8542 (mt) cc_final: 0.7905 (pt) REVERT: B 145 ARG cc_start: 0.8541 (mtm180) cc_final: 0.8258 (mtm180) REVERT: B 355 ILE cc_start: 0.8323 (mt) cc_final: 0.8031 (mm) REVERT: C 44 GLN cc_start: 0.8600 (tp40) cc_final: 0.8383 (tp40) REVERT: C 226 MET cc_start: 0.8994 (tpt) cc_final: 0.8562 (tpp) REVERT: D 139 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8026 (mt-10) REVERT: D 186 LYS cc_start: 0.9007 (tttp) cc_final: 0.8615 (ttmm) REVERT: E 445 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8401 (mt-10) REVERT: F 247 GLU cc_start: 0.6541 (pm20) cc_final: 0.6273 (pm20) REVERT: G 13 GLN cc_start: 0.8827 (pp30) cc_final: 0.8450 (pp30) REVERT: G 33 PHE cc_start: 0.8247 (m-80) cc_final: 0.8044 (m-80) REVERT: G 103 ARG cc_start: 0.8390 (ttm110) cc_final: 0.7524 (tpt90) REVERT: H 13 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8672 (pp30) REVERT: H 38 LYS cc_start: 0.8571 (mmtm) cc_final: 0.8334 (mttp) REVERT: I 218 ASN cc_start: 0.7351 (m-40) cc_final: 0.7139 (m110) REVERT: I 307 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7278 (mm-30) REVERT: J 44 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6894 (tp30) REVERT: J 170 MET cc_start: 0.5644 (OUTLIER) cc_final: 0.5319 (ttt) REVERT: J 216 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6867 (mmm) REVERT: J 318 LEU cc_start: 0.8217 (pt) cc_final: 0.7786 (tt) REVERT: K 86 MET cc_start: 0.7252 (ttm) cc_final: 0.7051 (ttp) REVERT: K 93 MET cc_start: 0.8887 (tmm) cc_final: 0.7542 (mpp) REVERT: K 110 LEU cc_start: 0.5203 (OUTLIER) cc_final: 0.4659 (tm) REVERT: L 182 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7341 (pp20) REVERT: L 183 HIS cc_start: 0.8823 (m-70) cc_final: 0.8133 (m90) outliers start: 88 outliers final: 56 residues processed: 318 average time/residue: 0.6541 time to fit residues: 242.8090 Evaluate side-chains 297 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 235 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 25 LYS Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain I residue 297 GLN Chi-restraints excluded: chain I residue 305 MET Chi-restraints excluded: chain I residue 311 SER Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 311 SER Chi-restraints excluded: chain K residue 14 ILE Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 183 HIS Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 133 SER Chi-restraints excluded: chain L residue 182 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 302 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 221 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 247 optimal weight: 9.9990 chunk 327 optimal weight: 0.0030 chunk 166 optimal weight: 2.9990 chunk 285 optimal weight: 0.0980 chunk 227 optimal weight: 3.9990 overall best weight: 2.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN C 277 GLN D 44 GLN F 470 HIS J 218 ASN L 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.108312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.070993 restraints weight = 117880.025| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.71 r_work: 0.2821 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 29257 Z= 0.241 Angle : 0.638 10.576 39649 Z= 0.324 Chirality : 0.048 0.172 4628 Planarity : 0.004 0.056 5049 Dihedral : 5.003 57.477 4003 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.13 % Favored : 94.84 % Rotamer: Outliers : 3.01 % Allowed : 19.26 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.24 (0.14), residues: 3622 helix: 1.40 (0.14), residues: 1476 sheet: -0.47 (0.25), residues: 460 loop : -0.74 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 292 TYR 0.025 0.002 TYR I 231 PHE 0.018 0.002 PHE D 177 TRP 0.015 0.001 TRP L 119 HIS 0.008 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00597 (29257) covalent geometry : angle 0.63782 (39649) hydrogen bonds : bond 0.04309 ( 1171) hydrogen bonds : angle 4.11898 ( 3317) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 239 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.8504 (ptp90) cc_final: 0.8281 (mtm-85) REVERT: A 359 ASN cc_start: 0.8981 (OUTLIER) cc_final: 0.8745 (m110) REVERT: B 127 LEU cc_start: 0.8632 (mt) cc_final: 0.8011 (pt) REVERT: B 145 ARG cc_start: 0.8539 (mtm180) cc_final: 0.8217 (mtm180) REVERT: B 355 ILE cc_start: 0.8285 (mt) cc_final: 0.7994 (mm) REVERT: D 139 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8051 (mt-10) REVERT: D 186 LYS cc_start: 0.9002 (tttp) cc_final: 0.8618 (ttmm) REVERT: E 445 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8439 (mt-10) REVERT: F 247 GLU cc_start: 0.6653 (pm20) cc_final: 0.6390 (pm20) REVERT: G 13 GLN cc_start: 0.8813 (pp30) cc_final: 0.8423 (pp30) REVERT: G 103 ARG cc_start: 0.8382 (ttm110) cc_final: 0.7572 (tpt90) REVERT: H 13 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8616 (pp30) REVERT: I 209 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7478 (tmmt) REVERT: I 218 ASN cc_start: 0.7391 (m-40) cc_final: 0.7170 (m110) REVERT: J 44 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6901 (tp30) REVERT: J 71 MET cc_start: 0.5050 (mtp) cc_final: 0.4430 (mtp) REVERT: J 170 MET cc_start: 0.5617 (OUTLIER) cc_final: 0.5289 (ttt) REVERT: J 209 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7166 (mmtp) REVERT: J 216 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6989 (tpt) REVERT: J 318 LEU cc_start: 0.8174 (pt) cc_final: 0.7813 (tt) REVERT: K 93 MET cc_start: 0.8916 (tmm) cc_final: 0.7564 (mpp) REVERT: K 141 GLN cc_start: 0.8525 (mp10) cc_final: 0.8322 (mp10) REVERT: K 205 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7938 (tp30) REVERT: L 135 ARG cc_start: 0.7783 (tmm160) cc_final: 0.7440 (tmm160) REVERT: L 173 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7782 (tm-30) REVERT: L 182 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7415 (pp20) REVERT: L 183 HIS cc_start: 0.8774 (m-70) cc_final: 0.8376 (m-70) outliers start: 94 outliers final: 59 residues processed: 315 average time/residue: 0.6927 time to fit residues: 253.8745 Evaluate side-chains 303 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 236 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain I residue 297 GLN Chi-restraints excluded: chain I residue 311 SER Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 162 SER Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 209 LYS Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 311 SER Chi-restraints excluded: chain K residue 14 ILE Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 183 HIS Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 133 SER Chi-restraints excluded: chain L residue 182 GLU Chi-restraints excluded: chain L residue 195 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 73 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 351 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 292 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN C 261 HIS C 277 GLN D 44 GLN F 470 HIS J 218 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.110709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.074677 restraints weight = 123113.526| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.82 r_work: 0.2868 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29257 Z= 0.123 Angle : 0.566 16.279 39649 Z= 0.285 Chirality : 0.044 0.162 4628 Planarity : 0.004 0.057 5049 Dihedral : 4.630 58.487 3999 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.41 % Allowed : 19.89 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3622 helix: 1.65 (0.14), residues: 1464 sheet: -0.22 (0.26), residues: 437 loop : -0.65 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 292 TYR 0.021 0.001 TYR I 231 PHE 0.017 0.001 PHE G 10 TRP 0.014 0.001 TRP L 119 HIS 0.009 0.001 HIS F 470 Details of bonding type rmsd covalent geometry : bond 0.00295 (29257) covalent geometry : angle 0.56561 (39649) hydrogen bonds : bond 0.03237 ( 1171) hydrogen bonds : angle 3.88348 ( 3317) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 244 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: B 127 LEU cc_start: 0.8601 (mt) cc_final: 0.7982 (pt) REVERT: B 145 ARG cc_start: 0.8575 (mtm180) cc_final: 0.8286 (mtm180) REVERT: B 355 ILE cc_start: 0.8308 (mt) cc_final: 0.8022 (mm) REVERT: D 139 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8033 (mt-10) REVERT: E 445 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8392 (mt-10) REVERT: F 247 GLU cc_start: 0.6539 (pm20) cc_final: 0.6258 (pm20) REVERT: F 328 SER cc_start: 0.8987 (OUTLIER) cc_final: 0.8533 (p) REVERT: G 13 GLN cc_start: 0.8749 (pp30) cc_final: 0.8356 (pp30) REVERT: G 103 ARG cc_start: 0.8402 (ttm110) cc_final: 0.7582 (tpt90) REVERT: H 13 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8729 (pp30) REVERT: I 218 ASN cc_start: 0.7346 (m-40) cc_final: 0.7127 (m110) REVERT: J 44 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6753 (tp30) REVERT: J 170 MET cc_start: 0.5478 (OUTLIER) cc_final: 0.5127 (ttt) REVERT: J 216 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.7059 (tpt) REVERT: J 318 LEU cc_start: 0.8217 (pt) cc_final: 0.7807 (tt) REVERT: K 93 MET cc_start: 0.8907 (tmm) cc_final: 0.7528 (mpp) REVERT: L 173 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7538 (tm-30) REVERT: L 182 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7529 (pp20) outliers start: 75 outliers final: 55 residues processed: 306 average time/residue: 0.6772 time to fit residues: 241.6259 Evaluate side-chains 298 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 237 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 470 HIS Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain I residue 297 GLN Chi-restraints excluded: chain I residue 311 SER Chi-restraints excluded: chain J residue 44 GLU Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 162 SER Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 311 SER Chi-restraints excluded: chain K residue 14 ILE Chi-restraints excluded: chain K residue 183 HIS Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 133 SER Chi-restraints excluded: chain L residue 182 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 313 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 210 optimal weight: 2.9990 chunk 246 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 359 ASN ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN C 277 GLN D 44 GLN F 470 HIS J 218 ASN L 59 ASN ** L 112 ASN ** 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 = 0.3613 r_free = 0.3613 target = 0.109376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.073278 restraints weight = 115409.335| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.77 r_work: 0.2845 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 29257 Z= 0.175 Angle : 0.613 15.475 39649 Z= 0.308 Chirality : 0.046 0.200 4628 Planarity : 0.004 0.056 5049 Dihedral : 4.695 57.927 3997 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.41 % Allowed : 20.15 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.14), residues: 3622 helix: 1.55 (0.14), residues: 1476 sheet: -0.36 (0.25), residues: 459 loop : -0.66 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 292 TYR 0.022 0.001 TYR I 231 PHE 0.023 0.001 PHE G 10 TRP 0.014 0.001 TRP L 119 HIS 0.009 0.001 HIS F 470 Details of bonding type rmsd covalent geometry : bond 0.00431 (29257) covalent geometry : angle 0.61258 (39649) hydrogen bonds : bond 0.03716 ( 1171) hydrogen bonds : angle 3.95353 ( 3317) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7244 Ramachandran restraints generated. 3622 Oldfield, 0 Emsley, 3622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 237 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: B 127 LEU cc_start: 0.8619 (mt) cc_final: 0.7994 (pt) REVERT: B 145 ARG cc_start: 0.8561 (mtm180) cc_final: 0.8270 (mtm180) REVERT: B 355 ILE cc_start: 0.8286 (mt) cc_final: 0.8005 (mm) REVERT: C 24 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7623 (mtp180) REVERT: C 44 GLN cc_start: 0.8495 (tp40) cc_final: 0.8265 (tp40) REVERT: C 48 ASP cc_start: 0.8244 (m-30) cc_final: 0.8024 (m-30) REVERT: D 139 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8043 (mt-10) REVERT: D 186 LYS cc_start: 0.9019 (tttp) cc_final: 0.8631 (ttmm) REVERT: E 445 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8416 (mt-10) REVERT: F 247 GLU cc_start: 0.6426 (pm20) cc_final: 0.6189 (pm20) REVERT: F 328 SER cc_start: 0.9010 (OUTLIER) cc_final: 0.8526 (p) REVERT: G 13 GLN cc_start: 0.8685 (pp30) cc_final: 0.8362 (pp30) REVERT: G 103 ARG cc_start: 0.8411 (ttm110) cc_final: 0.7573 (tpt90) REVERT: H 13 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8735 (pp30) REVERT: I 218 ASN cc_start: 0.7387 (m-40) cc_final: 0.7168 (m110) REVERT: J 170 MET cc_start: 0.5643 (OUTLIER) cc_final: 0.5299 (ttt) REVERT: J 209 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7110 (mmtp) REVERT: J 216 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6977 (tpt) REVERT: J 318 LEU cc_start: 0.8201 (pt) cc_final: 0.7763 (tt) REVERT: K 93 MET cc_start: 0.8915 (tmm) cc_final: 0.7553 (mpp) REVERT: K 110 LEU cc_start: 0.5365 (OUTLIER) cc_final: 0.4897 (tm) REVERT: L 135 ARG cc_start: 0.8010 (mpp-170) cc_final: 0.7262 (tmm160) REVERT: L 173 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7629 (tm-30) REVERT: L 175 ARG cc_start: 0.8417 (mpp80) cc_final: 0.8195 (mpp80) REVERT: L 182 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7261 (pp20) REVERT: L 183 HIS cc_start: 0.8685 (m-70) cc_final: 0.7861 (m90) outliers start: 75 outliers final: 57 residues processed: 300 average time/residue: 0.6943 time to fit residues: 243.3372 Evaluate side-chains 300 residues out of total 3218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 235 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain E residue 509 CYS Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 509 CYS Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain I residue 297 GLN Chi-restraints excluded: chain I residue 311 SER Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 162 SER Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 209 LYS Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 311 SER Chi-restraints excluded: chain K residue 14 ILE Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 183 HIS Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 133 SER Chi-restraints excluded: chain L residue 182 GLU Chi-restraints excluded: chain L residue 195 SER Chi-restraints excluded: chain L residue 198 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 190 optimal weight: 0.0770 chunk 303 optimal weight: 6.9990 chunk 251 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 355 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 243 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN C 277 GLN D 44 GLN F 470 HIS J 218 ASN L 59 ASN ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.111673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.075786 restraints weight = 101400.424| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.39 r_work: 0.2911 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29257 Z= 0.111 Angle : 0.565 16.291 39649 Z= 0.284 Chirality : 0.044 0.210 4628 Planarity : 0.004 0.056 5049 Dihedral : 4.493 59.363 3997 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.00 % Allowed : 20.65 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.15), residues: 3622 helix: 1.74 (0.14), residues: 1466 sheet: -0.18 (0.26), residues: 440 loop : -0.56 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 292 TYR 0.022 0.001 TYR I 231 PHE 0.025 0.001 PHE G 10 TRP 0.012 0.001 TRP L 119 HIS 0.012 0.001 HIS F 470 Details of bonding type rmsd covalent geometry : bond 0.00262 (29257) covalent geometry : angle 0.56510 (39649) hydrogen bonds : bond 0.03018 ( 1171) hydrogen bonds : angle 3.81320 ( 3317) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11919.89 seconds wall clock time: 203 minutes 6.16 seconds (12186.16 seconds total)