Starting phenix.real_space_refine on Wed Mar 4 12:04:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qlf_4581/03_2026/6qlf_4581.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qlf_4581/03_2026/6qlf_4581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qlf_4581/03_2026/6qlf_4581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qlf_4581/03_2026/6qlf_4581.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qlf_4581/03_2026/6qlf_4581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qlf_4581/03_2026/6qlf_4581.map" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 76 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 8639 2.51 5 N 2348 2.21 5 O 2461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.01s 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: 13501 Number of models: 1 Model: "" Number of chains: 8 Chain: "L" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1939 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 231} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2923 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 20, 'TRANS': 350} Chain breaks: 5 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 76 Chain: "O" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1658 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "P" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1795 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "Q" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1421 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain breaks: 3 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 15, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 156 Chain: "U" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1229 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 11, 'PHE:plan': 3, 'ASN:plan1': 3, 'GLU:plan': 6, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "Y" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1541 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 15, 'TYR:plan': 1, 'GLU:plan': 16, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 138 Chain: "Z" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 995 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'GLN:plan1': 5, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 118 Time building chain proxies: 3.52, per 1000 atoms: 0.26 Number of scatterers: 13501 At special positions: 0 Unit cell: (139.52, 164.59, 134.07, 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 53 16.00 O 2461 8.00 N 2348 7.00 C 8639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 678.8 milliseconds 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3438 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 13 sheets defined 56.1% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'L' and resid 19 through 28 Processing helix chain 'L' and resid 95 through 108 removed outlier: 3.573A pdb=" N TYR L 107 " --> pdb=" O LEU L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 128 Processing helix chain 'L' and resid 153 through 157 removed outlier: 3.596A pdb=" N LYS L 156 " --> pdb=" O THR L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 178 Processing helix chain 'L' and resid 182 through 187 Processing helix chain 'L' and resid 187 through 197 Processing helix chain 'L' and resid 229 through 240 removed outlier: 3.645A pdb=" N LEU L 233 " --> pdb=" O ARG L 229 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE L 240 " --> pdb=" O VAL L 236 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 25 removed outlier: 4.024A pdb=" N VAL N 20 " --> pdb=" O ASP N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 43 removed outlier: 3.510A pdb=" N LEU N 32 " --> pdb=" O PRO N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 65 removed outlier: 3.630A pdb=" N ASP N 59 " --> pdb=" O THR N 55 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU N 60 " --> pdb=" O GLU N 56 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU N 61 " --> pdb=" O THR N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 77 removed outlier: 3.655A pdb=" N ILE N 71 " --> pdb=" O ARG N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 100 Processing helix chain 'N' and resid 101 through 104 removed outlier: 3.784A pdb=" N PHE N 104 " --> pdb=" O PRO N 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 101 through 104' Processing helix chain 'N' and resid 126 through 138 removed outlier: 3.806A pdb=" N GLU N 130 " --> pdb=" O ALA N 126 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN N 131 " --> pdb=" O LYS N 127 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS N 138 " --> pdb=" O THR N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 218 through 232 removed outlier: 3.849A pdb=" N ARG N 222 " --> pdb=" O ASP N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 259 removed outlier: 3.977A pdb=" N ILE N 254 " --> pdb=" O SER N 250 " (cutoff:3.500A) Processing helix chain 'N' and resid 261 through 265 removed outlier: 3.551A pdb=" N ALA N 264 " --> pdb=" O SER N 261 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU N 265 " --> pdb=" O ARG N 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 261 through 265' Processing helix chain 'N' and resid 268 through 273 removed outlier: 4.301A pdb=" N CYS N 272 " --> pdb=" O PRO N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 289 through 294 Processing helix chain 'N' and resid 318 through 334 Processing helix chain 'N' and resid 408 through 419 Processing helix chain 'N' and resid 428 through 433 removed outlier: 3.637A pdb=" N GLY N 433 " --> pdb=" O GLY N 429 " (cutoff:3.500A) Processing helix chain 'O' and resid 155 through 172 Processing helix chain 'O' and resid 245 through 253 Processing helix chain 'O' and resid 254 through 257 removed outlier: 3.890A pdb=" N LEU O 257 " --> pdb=" O ASN O 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 254 through 257' Processing helix chain 'O' and resid 260 through 291 removed outlier: 3.761A pdb=" N PHE O 267 " --> pdb=" O ASP O 263 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE O 285 " --> pdb=" O ARG O 281 " (cutoff:3.500A) Processing helix chain 'O' and resid 340 through 349 removed outlier: 3.801A pdb=" N TRP O 344 " --> pdb=" O ASN O 340 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU O 348 " --> pdb=" O TRP O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 352 through 360 removed outlier: 3.878A pdb=" N GLU O 356 " --> pdb=" O LEU O 352 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN O 360 " --> pdb=" O GLU O 356 " (cutoff:3.500A) Processing helix chain 'P' and resid 133 through 140 removed outlier: 3.565A pdb=" N THR P 140 " --> pdb=" O LYS P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 160 removed outlier: 3.737A pdb=" N HIS P 160 " --> pdb=" O TYR P 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 226 through 231 removed outlier: 4.218A pdb=" N GLN P 230 " --> pdb=" O LEU P 226 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU P 231 " --> pdb=" O LYS P 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 226 through 231' Processing helix chain 'P' and resid 232 through 234 No H-bonds generated for 'chain 'P' and resid 232 through 234' Processing helix chain 'P' and resid 236 through 264 Processing helix chain 'P' and resid 333 through 348 Processing helix chain 'P' and resid 352 through 363 removed outlier: 3.726A pdb=" N GLU P 356 " --> pdb=" O THR P 352 " (cutoff:3.500A) Processing helix chain 'Q' and resid 162 through 184 removed outlier: 3.657A pdb=" N GLU Q 182 " --> pdb=" O PHE Q 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 199 removed outlier: 3.809A pdb=" N ARG Q 198 " --> pdb=" O ASN Q 194 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE Q 199 " --> pdb=" O GLU Q 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 194 through 199' Processing helix chain 'Q' and resid 200 through 217 removed outlier: 3.716A pdb=" N GLU Q 204 " --> pdb=" O TYR Q 200 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS Q 217 " --> pdb=" O LYS Q 213 " (cutoff:3.500A) Processing helix chain 'Q' and resid 233 through 293 removed outlier: 3.861A pdb=" N ILE Q 237 " --> pdb=" O ASP Q 233 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU Q 291 " --> pdb=" O LEU Q 287 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE Q 292 " --> pdb=" O THR Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 323 through 333 removed outlier: 3.694A pdb=" N ASN Q 327 " --> pdb=" O VAL Q 323 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU Q 332 " --> pdb=" O ASP Q 328 " (cutoff:3.500A) Processing helix chain 'Q' and resid 349 through 357 Processing helix chain 'Q' and resid 359 through 381 Processing helix chain 'Q' and resid 382 through 391 removed outlier: 3.728A pdb=" N LYS Q 387 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU Q 388 " --> pdb=" O GLU Q 384 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL Q 391 " --> pdb=" O LYS Q 387 " (cutoff:3.500A) Processing helix chain 'U' and resid 132 through 156 Proline residue: U 152 - end of helix Processing helix chain 'U' and resid 170 through 232 removed outlier: 4.315A pdb=" N ASP U 174 " --> pdb=" O LEU U 170 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA U 232 " --> pdb=" O GLN U 228 " (cutoff:3.500A) Processing helix chain 'U' and resid 233 through 265 removed outlier: 3.564A pdb=" N HIS U 237 " --> pdb=" O GLY U 233 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU U 264 " --> pdb=" O THR U 260 " (cutoff:3.500A) Processing helix chain 'U' and resid 288 through 299 Processing helix chain 'U' and resid 305 through 318 removed outlier: 3.595A pdb=" N ILE U 309 " --> pdb=" O LEU U 305 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE U 312 " --> pdb=" O LYS U 308 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU U 314 " --> pdb=" O ASN U 310 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN U 315 " --> pdb=" O LYS U 311 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 16 removed outlier: 3.911A pdb=" N SER Y 7 " --> pdb=" O ASP Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 32 removed outlier: 4.078A pdb=" N ALA Y 31 " --> pdb=" O ASP Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 57 through 82 removed outlier: 3.654A pdb=" N LEU Y 61 " --> pdb=" O GLY Y 57 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER Y 76 " --> pdb=" O GLU Y 72 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET Y 82 " --> pdb=" O SER Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 103 removed outlier: 3.669A pdb=" N GLU Y 102 " --> pdb=" O ARG Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 110 through 118 Processing helix chain 'Y' and resid 137 through 186 Processing helix chain 'Y' and resid 189 through 196 Processing helix chain 'Y' and resid 196 through 214 removed outlier: 3.543A pdb=" N VAL Y 203 " --> pdb=" O GLY Y 199 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA Y 204 " --> pdb=" O LYS Y 200 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU Y 210 " --> pdb=" O GLU Y 206 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU Y 211 " --> pdb=" O GLU Y 207 " (cutoff:3.500A) Processing helix chain 'Y' and resid 223 through 236 removed outlier: 3.923A pdb=" N GLU Y 227 " --> pdb=" O PRO Y 223 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 13 removed outlier: 3.977A pdb=" N ASN Z 9 " --> pdb=" O GLN Z 5 " (cutoff:3.500A) Processing helix chain 'Z' and resid 19 through 24 removed outlier: 3.907A pdb=" N GLN Z 23 " --> pdb=" O LEU Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 39 through 50 removed outlier: 4.269A pdb=" N TYR Z 43 " --> pdb=" O LEU Z 39 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU Z 45 " --> pdb=" O HIS Z 41 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN Z 47 " --> pdb=" O TYR Z 43 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 57 Processing helix chain 'Z' and resid 57 through 81 removed outlier: 3.663A pdb=" N PHE Z 65 " --> pdb=" O ILE Z 61 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE Z 75 " --> pdb=" O ARG Z 71 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU Z 81 " --> pdb=" O GLU Z 77 " (cutoff:3.500A) Processing helix chain 'Z' and resid 88 through 124 removed outlier: 3.836A pdb=" N ASN Z 124 " --> pdb=" O ALA Z 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 134 through 152 Processing sheet with id=AA1, first strand: chain 'L' and resid 35 through 36 removed outlier: 3.553A pdb=" N GLN L 36 " --> pdb=" O ARG L 55 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR L 56 " --> pdb=" O PHE L 75 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET L 85 " --> pdb=" O ILE L 10 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR L 223 " --> pdb=" O TYR L 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 130 through 131 removed outlier: 3.605A pdb=" N GLN L 139 " --> pdb=" O HIS L 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 161 through 164 removed outlier: 6.421A pdb=" N LYS L 146 " --> pdb=" O VAL L 208 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL L 208 " --> pdb=" O LYS L 146 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TYR L 148 " --> pdb=" O THR L 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 117 through 118 removed outlier: 3.618A pdb=" N LYS N 117 " --> pdb=" O ARG N 113 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE N 210 " --> pdb=" O PRO N 205 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR N 201 " --> pdb=" O SER N 214 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 141 through 146 removed outlier: 4.008A pdb=" N HIS N 141 " --> pdb=" O PHE N 162 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR N 201 " --> pdb=" O SER N 214 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE N 210 " --> pdb=" O PRO N 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 295 through 298 removed outlier: 3.671A pdb=" N LYS N 295 " --> pdb=" O ILE P 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 384 through 385 removed outlier: 3.622A pdb=" N VAL N 385 " --> pdb=" O PHE N 404 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 398 through 400 removed outlier: 3.594A pdb=" N ILE N 398 " --> pdb=" O ASN N 391 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR N 388 " --> pdb=" O ILE N 442 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET N 443 " --> pdb=" O ASP N 446 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 175 through 180 removed outlier: 4.166A pdb=" N LEU O 180 " --> pdb=" O MET O 201 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET O 201 " --> pdb=" O LEU O 180 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS O 225 " --> pdb=" O LEU O 235 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU O 235 " --> pdb=" O LYS O 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 186 through 188 Processing sheet with id=AB2, first strand: chain 'O' and resid 305 through 309 removed outlier: 3.839A pdb=" N LYS O 314 " --> pdb=" O LEU O 330 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU O 330 " --> pdb=" O LYS O 314 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS O 320 " --> pdb=" O ILE O 324 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE O 324 " --> pdb=" O LYS O 320 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 168 through 172 removed outlier: 5.425A pdb=" N VAL P 169 " --> pdb=" O ASN P 186 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN P 186 " --> pdb=" O VAL P 169 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL P 185 " --> pdb=" O PHE P 201 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE P 197 " --> pdb=" O PHE P 189 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU P 198 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ILE P 220 " --> pdb=" O GLU P 198 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLN P 200 " --> pdb=" O LEU P 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 270 through 272 removed outlier: 3.563A pdb=" N MET P 318 " --> pdb=" O THR P 303 " (cutoff:3.500A) 794 hydrogen bonds defined for protein. 2334 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4207 1.34 - 1.46: 2284 1.46 - 1.58: 7119 1.58 - 1.70: 1 1.70 - 1.82: 87 Bond restraints: 13698 Sorted by residual: bond pdb=" CA THR N 14 " pdb=" CB THR N 14 " ideal model delta sigma weight residual 1.529 1.591 -0.062 1.43e-02 4.89e+03 1.89e+01 bond pdb=" N MET P 274 " pdb=" CA MET P 274 " ideal model delta sigma weight residual 1.455 1.490 -0.036 1.25e-02 6.40e+03 8.10e+00 bond pdb=" N VAL L 40 " pdb=" CA VAL L 40 " ideal model delta sigma weight residual 1.461 1.495 -0.033 1.23e-02 6.61e+03 7.39e+00 bond pdb=" N LEU Q 296 " pdb=" CA LEU Q 296 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.27e-02 6.20e+03 5.68e+00 bond pdb=" N ASN P 275 " pdb=" CA ASN P 275 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.08e+00 ... (remaining 13693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 17843 1.94 - 3.89: 600 3.89 - 5.83: 58 5.83 - 7.78: 25 7.78 - 9.72: 7 Bond angle restraints: 18533 Sorted by residual: angle pdb=" N ILE U 283 " pdb=" CA ILE U 283 " pdb=" C ILE U 283 " ideal model delta sigma weight residual 112.96 106.94 6.02 1.00e+00 1.00e+00 3.63e+01 angle pdb=" N VAL P 224 " pdb=" CA VAL P 224 " pdb=" C VAL P 224 " ideal model delta sigma weight residual 112.17 107.28 4.89 9.50e-01 1.11e+00 2.65e+01 angle pdb=" N VAL O 310 " pdb=" CA VAL O 310 " pdb=" C VAL O 310 " ideal model delta sigma weight residual 109.34 99.62 9.72 2.08e+00 2.31e-01 2.18e+01 angle pdb=" C GLU L 135 " pdb=" N ASN L 136 " pdb=" CA ASN L 136 " ideal model delta sigma weight residual 121.54 130.04 -8.50 1.91e+00 2.74e-01 1.98e+01 angle pdb=" C ILE N 393 " pdb=" N ASN N 394 " pdb=" CA ASN N 394 " ideal model delta sigma weight residual 121.54 129.66 -8.12 1.91e+00 2.74e-01 1.81e+01 ... (remaining 18528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 7366 17.67 - 35.34: 826 35.34 - 53.00: 133 53.00 - 70.67: 26 70.67 - 88.34: 11 Dihedral angle restraints: 8362 sinusoidal: 3113 harmonic: 5249 Sorted by residual: dihedral pdb=" CA TYR N 77 " pdb=" C TYR N 77 " pdb=" N VAL N 78 " pdb=" CA VAL N 78 " ideal model delta harmonic sigma weight residual 180.00 151.60 28.40 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ASP P 209 " pdb=" C ASP P 209 " pdb=" N SER P 210 " pdb=" CA SER P 210 " ideal model delta harmonic sigma weight residual -180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA GLU P 208 " pdb=" C GLU P 208 " pdb=" N ASP P 209 " pdb=" CA ASP P 209 " ideal model delta harmonic sigma weight residual -180.00 -154.80 -25.20 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 8359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1577 0.043 - 0.086: 459 0.086 - 0.129: 144 0.129 - 0.172: 33 0.172 - 0.215: 8 Chirality restraints: 2221 Sorted by residual: chirality pdb=" CA ASN N 394 " pdb=" N ASN N 394 " pdb=" C ASN N 394 " pdb=" CB ASN N 394 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA VAL O 310 " pdb=" N VAL O 310 " pdb=" C VAL O 310 " pdb=" CB VAL O 310 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB VAL P 224 " pdb=" CA VAL P 224 " pdb=" CG1 VAL P 224 " pdb=" CG2 VAL P 224 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 2218 not shown) Planarity restraints: 2336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU P 273 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.00e+00 pdb=" C LEU P 273 " 0.046 2.00e-02 2.50e+03 pdb=" O LEU P 273 " -0.017 2.00e-02 2.50e+03 pdb=" N MET P 274 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU N 152 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO N 153 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO N 153 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO N 153 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU P 145 " -0.036 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO P 146 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO P 146 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO P 146 " -0.031 5.00e-02 4.00e+02 ... (remaining 2333 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3821 2.81 - 3.33: 11635 3.33 - 3.86: 21378 3.86 - 4.38: 22977 4.38 - 4.90: 41963 Nonbonded interactions: 101774 Sorted by model distance: nonbonded pdb=" OH TYR U 302 " pdb=" OE1 GLU Y 183 " model vdw 2.290 3.040 nonbonded pdb=" O SER O 153 " pdb=" OG SER O 153 " model vdw 2.326 3.040 nonbonded pdb=" OG SER N 46 " pdb=" O VAL N 78 " model vdw 2.341 3.040 nonbonded pdb=" OG1 THR L 133 " pdb=" O ILE L 137 " model vdw 2.350 3.040 nonbonded pdb=" OG1 THR Q 364 " pdb=" OG SER U 282 " model vdw 2.351 3.040 ... (remaining 101769 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.710 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.005 0.062 13698 Z= 0.233 Angle : 0.828 9.722 18533 Z= 0.481 Chirality : 0.048 0.215 2221 Planarity : 0.005 0.056 2336 Dihedral : 15.137 88.340 4924 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.14 % Favored : 94.69 % Rotamer: Outliers : 0.44 % Allowed : 6.80 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.91 (0.16), residues: 1733 helix: -2.03 (0.13), residues: 917 sheet: -2.94 (0.30), residues: 222 loop : -3.09 (0.20), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 375 TYR 0.028 0.002 TYR P 156 PHE 0.020 0.002 PHE L 161 TRP 0.013 0.002 TRP U 236 HIS 0.006 0.001 HIS U 237 Details of bonding type rmsd covalent geometry : bond 0.00472 (13698) covalent geometry : angle 0.82751 (18533) hydrogen bonds : bond 0.18103 ( 781) hydrogen bonds : angle 7.45452 ( 2334) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 309 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: L 32 ASP cc_start: 0.7762 (p0) cc_final: 0.7541 (p0) REVERT: L 34 ASP cc_start: 0.7090 (p0) cc_final: 0.6683 (p0) REVERT: L 160 GLN cc_start: 0.8045 (pp30) cc_final: 0.7811 (pt0) REVERT: N 97 MET cc_start: 0.8043 (ttm) cc_final: 0.7827 (ttm) REVERT: N 403 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7699 (mttp) REVERT: O 252 ASP cc_start: 0.8119 (t0) cc_final: 0.7732 (t0) REVERT: P 318 MET cc_start: 0.7701 (ptm) cc_final: 0.7488 (ptt) REVERT: Q 264 ARG cc_start: 0.8009 (ttm-80) cc_final: 0.7787 (tpp80) REVERT: Q 266 GLN cc_start: 0.8234 (tp40) cc_final: 0.7932 (mm-40) REVERT: Q 270 GLU cc_start: 0.7623 (tp30) cc_final: 0.7173 (tp30) REVERT: Q 274 LYS cc_start: 0.7262 (pptt) cc_final: 0.6921 (tppt) REVERT: U 218 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7830 (tm-30) REVERT: U 249 LYS cc_start: 0.8269 (mttt) cc_final: 0.7865 (mptt) REVERT: U 251 LYS cc_start: 0.9213 (mmmt) cc_final: 0.8788 (mmmt) REVERT: U 254 LYS cc_start: 0.8384 (ttmt) cc_final: 0.8075 (ttpt) REVERT: U 285 ASP cc_start: 0.8599 (t70) cc_final: 0.8365 (t0) REVERT: U 308 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8202 (mttp) REVERT: Y 64 LYS cc_start: 0.8331 (tptp) cc_final: 0.8063 (tptp) REVERT: Y 180 SER cc_start: 0.8435 (t) cc_final: 0.8224 (t) REVERT: Z 20 ILE cc_start: 0.6669 (OUTLIER) cc_final: 0.6299 (mp) REVERT: Z 62 LYS cc_start: 0.8384 (tttt) cc_final: 0.7692 (mtpt) outliers start: 6 outliers final: 3 residues processed: 314 average time/residue: 0.1559 time to fit residues: 65.7760 Evaluate side-chains 235 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 231 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain Z residue 20 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 ASN L 96 ASN N 165 ASN N 213 HIS N 226 GLN N 277 ASN N 435 ASN O 274 GLN O 322 ASN P 135 GLN P 297 GLN Q 245 GLN U 257 ASN Y 158 GLN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 198 ASN Z 47 GLN Z 113 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.149702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110304 restraints weight = 18773.762| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.02 r_work: 0.3082 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13698 Z= 0.225 Angle : 0.618 10.651 18533 Z= 0.325 Chirality : 0.043 0.204 2221 Planarity : 0.004 0.053 2336 Dihedral : 5.221 57.259 1896 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.77 % Favored : 94.11 % Rotamer: Outliers : 2.56 % Allowed : 14.56 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.19), residues: 1733 helix: 0.12 (0.17), residues: 942 sheet: -2.30 (0.33), residues: 223 loop : -2.71 (0.22), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 197 TYR 0.016 0.002 TYR Q 363 PHE 0.020 0.002 PHE O 178 TRP 0.011 0.001 TRP L 112 HIS 0.005 0.001 HIS U 237 Details of bonding type rmsd covalent geometry : bond 0.00540 (13698) covalent geometry : angle 0.61833 (18533) hydrogen bonds : bond 0.04866 ( 781) hydrogen bonds : angle 4.74092 ( 2334) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: L 32 ASP cc_start: 0.7877 (p0) cc_final: 0.7515 (p0) REVERT: L 34 ASP cc_start: 0.7660 (p0) cc_final: 0.7318 (p0) REVERT: L 58 MET cc_start: 0.8596 (tmm) cc_final: 0.8368 (tmm) REVERT: N 330 MET cc_start: 0.9297 (tpp) cc_final: 0.9039 (tpt) REVERT: O 252 ASP cc_start: 0.8646 (t0) cc_final: 0.8221 (t0) REVERT: P 150 MET cc_start: 0.8701 (tpp) cc_final: 0.8349 (mmt) REVERT: P 318 MET cc_start: 0.8764 (ptm) cc_final: 0.8551 (ptt) REVERT: P 348 TYR cc_start: 0.8577 (m-10) cc_final: 0.8282 (m-80) REVERT: Q 271 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7948 (mt-10) REVERT: Q 376 GLN cc_start: 0.8092 (tp40) cc_final: 0.7816 (pt0) REVERT: U 176 ARG cc_start: 0.7590 (mtt180) cc_final: 0.6779 (mmt-90) REVERT: U 218 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8426 (tm-30) REVERT: U 249 LYS cc_start: 0.8346 (mttt) cc_final: 0.7889 (mptt) REVERT: U 251 LYS cc_start: 0.9161 (mmmt) cc_final: 0.8820 (mmmt) REVERT: U 285 ASP cc_start: 0.8964 (t70) cc_final: 0.8633 (t0) REVERT: Y 15 GLU cc_start: 0.8588 (tp30) cc_final: 0.8295 (tp30) REVERT: Y 158 GLN cc_start: 0.8330 (mt0) cc_final: 0.8115 (mt0) REVERT: Z 52 ARG cc_start: 0.7461 (ttp80) cc_final: 0.7231 (ttp-170) REVERT: Z 58 GLU cc_start: 0.7822 (tt0) cc_final: 0.7531 (mm-30) REVERT: Z 62 LYS cc_start: 0.8158 (tttt) cc_final: 0.7400 (mtmt) outliers start: 35 outliers final: 24 residues processed: 265 average time/residue: 0.1424 time to fit residues: 51.7920 Evaluate side-chains 251 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 94 ASN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 278 VAL Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 346 ILE Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 281 THR Chi-restraints excluded: chain Q residue 296 LEU Chi-restraints excluded: chain Q residue 299 VAL Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 260 THR Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain Y residue 179 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 45 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 131 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 145 optimal weight: 0.0040 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 277 ASN O 274 GLN O 322 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 198 ASN Z 83 HIS Z 103 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.152054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111024 restraints weight = 18787.094| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.11 r_work: 0.3105 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13698 Z= 0.138 Angle : 0.529 9.840 18533 Z= 0.277 Chirality : 0.040 0.159 2221 Planarity : 0.003 0.039 2336 Dihedral : 4.647 50.530 1894 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.21 % Favored : 95.67 % Rotamer: Outliers : 2.49 % Allowed : 17.85 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.21), residues: 1733 helix: 1.04 (0.18), residues: 934 sheet: -1.93 (0.34), residues: 222 loop : -2.42 (0.23), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 98 TYR 0.015 0.001 TYR Y 193 PHE 0.014 0.001 PHE O 178 TRP 0.012 0.001 TRP L 102 HIS 0.004 0.001 HIS U 237 Details of bonding type rmsd covalent geometry : bond 0.00315 (13698) covalent geometry : angle 0.52854 (18533) hydrogen bonds : bond 0.04154 ( 781) hydrogen bonds : angle 4.32821 ( 2334) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 242 time to evaluate : 0.515 Fit side-chains REVERT: L 34 ASP cc_start: 0.7616 (p0) cc_final: 0.7325 (p0) REVERT: L 58 MET cc_start: 0.8595 (tmm) cc_final: 0.8348 (tmm) REVERT: L 111 MET cc_start: 0.8745 (mtt) cc_final: 0.8368 (mtt) REVERT: N 84 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7762 (mt) REVERT: N 255 MET cc_start: 0.9035 (mmm) cc_final: 0.8819 (mmm) REVERT: O 252 ASP cc_start: 0.8724 (t0) cc_final: 0.8309 (t0) REVERT: P 150 MET cc_start: 0.8757 (tpp) cc_final: 0.8397 (mmt) REVERT: P 318 MET cc_start: 0.8815 (ptm) cc_final: 0.8605 (ptt) REVERT: P 348 TYR cc_start: 0.8508 (m-10) cc_final: 0.8248 (m-80) REVERT: Q 270 GLU cc_start: 0.8087 (tp30) cc_final: 0.7452 (tp30) REVERT: Q 271 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8019 (mt-10) REVERT: Q 376 GLN cc_start: 0.8045 (tp40) cc_final: 0.7763 (pt0) REVERT: U 176 ARG cc_start: 0.7622 (mtt180) cc_final: 0.6675 (mmt-90) REVERT: U 218 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8497 (tm-30) REVERT: U 251 LYS cc_start: 0.9077 (mmmt) cc_final: 0.8813 (mmmt) REVERT: U 285 ASP cc_start: 0.8989 (t70) cc_final: 0.8643 (t0) REVERT: U 286 ASP cc_start: 0.8514 (t0) cc_final: 0.7821 (p0) REVERT: U 299 MET cc_start: 0.8499 (mmm) cc_final: 0.8059 (mmm) REVERT: Y 15 GLU cc_start: 0.8550 (tp30) cc_final: 0.8298 (tp30) REVERT: Y 120 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7721 (pp) REVERT: Z 52 ARG cc_start: 0.7478 (ttp80) cc_final: 0.7274 (ttp-170) REVERT: Z 62 LYS cc_start: 0.8172 (tttt) cc_final: 0.7489 (mtmt) REVERT: Z 102 GLN cc_start: 0.8206 (tp40) cc_final: 0.7942 (tp-100) REVERT: Z 113 GLN cc_start: 0.8226 (tp-100) cc_final: 0.7977 (mt0) outliers start: 34 outliers final: 21 residues processed: 266 average time/residue: 0.1400 time to fit residues: 51.2960 Evaluate side-chains 256 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 281 THR Chi-restraints excluded: chain Q residue 296 LEU Chi-restraints excluded: chain Q residue 299 VAL Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain Y residue 113 LEU Chi-restraints excluded: chain Y residue 120 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 135 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 252 HIS O 322 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.151798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111066 restraints weight = 18851.343| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.07 r_work: 0.3103 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13698 Z= 0.151 Angle : 0.524 9.439 18533 Z= 0.275 Chirality : 0.041 0.245 2221 Planarity : 0.003 0.039 2336 Dihedral : 4.460 42.390 1892 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.25 % Favored : 94.63 % Rotamer: Outliers : 3.15 % Allowed : 19.17 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.21), residues: 1733 helix: 1.47 (0.18), residues: 935 sheet: -1.60 (0.34), residues: 230 loop : -2.31 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 74 TYR 0.018 0.001 TYR Y 193 PHE 0.016 0.001 PHE O 178 TRP 0.012 0.001 TRP L 102 HIS 0.003 0.001 HIS U 237 Details of bonding type rmsd covalent geometry : bond 0.00357 (13698) covalent geometry : angle 0.52444 (18533) hydrogen bonds : bond 0.04073 ( 781) hydrogen bonds : angle 4.15780 ( 2334) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 238 time to evaluate : 0.591 Fit side-chains REVERT: L 34 ASP cc_start: 0.7605 (p0) cc_final: 0.7331 (p0) REVERT: L 111 MET cc_start: 0.8853 (mtt) cc_final: 0.8567 (mtt) REVERT: N 84 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7750 (mt) REVERT: N 255 MET cc_start: 0.9048 (mmm) cc_final: 0.8780 (mmm) REVERT: N 330 MET cc_start: 0.9317 (tpp) cc_final: 0.9039 (tpt) REVERT: O 252 ASP cc_start: 0.8771 (t0) cc_final: 0.8349 (t0) REVERT: O 323 GLU cc_start: 0.8285 (pt0) cc_final: 0.8005 (pt0) REVERT: P 150 MET cc_start: 0.8764 (tpp) cc_final: 0.8414 (mmt) REVERT: P 318 MET cc_start: 0.8832 (ptm) cc_final: 0.8616 (ptt) REVERT: P 348 TYR cc_start: 0.8543 (m-10) cc_final: 0.8303 (m-80) REVERT: Q 270 GLU cc_start: 0.8147 (tp30) cc_final: 0.7529 (tp30) REVERT: Q 271 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8109 (mt-10) REVERT: Q 364 THR cc_start: 0.9224 (m) cc_final: 0.9017 (p) REVERT: Q 376 GLN cc_start: 0.7896 (tp40) cc_final: 0.7635 (pt0) REVERT: U 176 ARG cc_start: 0.7632 (mtt180) cc_final: 0.6680 (mmt-90) REVERT: U 218 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8522 (tm-30) REVERT: U 251 LYS cc_start: 0.9063 (mmmt) cc_final: 0.8807 (mmmt) REVERT: U 285 ASP cc_start: 0.9005 (t70) cc_final: 0.8669 (t0) REVERT: Y 15 GLU cc_start: 0.8478 (tp30) cc_final: 0.8194 (tp30) REVERT: Y 120 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7652 (pp) REVERT: Z 43 TYR cc_start: 0.6604 (p90) cc_final: 0.5041 (t80) REVERT: Z 60 ARG cc_start: 0.8444 (tpt170) cc_final: 0.8225 (tpt170) REVERT: Z 62 LYS cc_start: 0.8141 (tttt) cc_final: 0.7538 (mtmt) outliers start: 43 outliers final: 27 residues processed: 268 average time/residue: 0.1369 time to fit residues: 51.0254 Evaluate side-chains 258 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 223 LEU Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 274 LYS Chi-restraints excluded: chain Q residue 281 THR Chi-restraints excluded: chain Q residue 299 VAL Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 228 GLN Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain Y residue 113 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Z residue 103 GLN Chi-restraints excluded: chain Z residue 126 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 40 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 172 optimal weight: 0.4980 chunk 83 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 165 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 173 optimal weight: 0.0000 chunk 127 optimal weight: 0.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 322 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 198 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.153734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114612 restraints weight = 18775.173| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.07 r_work: 0.3131 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13698 Z= 0.112 Angle : 0.506 10.130 18533 Z= 0.260 Chirality : 0.040 0.186 2221 Planarity : 0.003 0.035 2336 Dihedral : 4.160 31.502 1892 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.39 % Favored : 95.50 % Rotamer: Outliers : 2.49 % Allowed : 20.63 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.21), residues: 1733 helix: 1.76 (0.18), residues: 934 sheet: -1.39 (0.34), residues: 230 loop : -2.17 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 74 TYR 0.015 0.001 TYR Y 193 PHE 0.012 0.001 PHE O 178 TRP 0.013 0.001 TRP L 102 HIS 0.003 0.001 HIS U 237 Details of bonding type rmsd covalent geometry : bond 0.00251 (13698) covalent geometry : angle 0.50578 (18533) hydrogen bonds : bond 0.03758 ( 781) hydrogen bonds : angle 3.98555 ( 2334) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: L 34 ASP cc_start: 0.7536 (p0) cc_final: 0.7248 (p0) REVERT: L 95 ARG cc_start: 0.7941 (mtm-85) cc_final: 0.7655 (ttm170) REVERT: L 160 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8066 (pp30) REVERT: N 255 MET cc_start: 0.8994 (mmm) cc_final: 0.8759 (mmm) REVERT: O 252 ASP cc_start: 0.8755 (t0) cc_final: 0.8331 (t0) REVERT: O 323 GLU cc_start: 0.8273 (pt0) cc_final: 0.8020 (pt0) REVERT: P 150 MET cc_start: 0.8772 (tpp) cc_final: 0.8462 (mmt) REVERT: P 318 MET cc_start: 0.8830 (ptm) cc_final: 0.8606 (ptt) REVERT: P 348 TYR cc_start: 0.8557 (m-10) cc_final: 0.8345 (m-80) REVERT: Q 266 GLN cc_start: 0.8436 (tp40) cc_final: 0.8072 (mm-40) REVERT: Q 270 GLU cc_start: 0.8149 (tp30) cc_final: 0.7541 (tp30) REVERT: Q 271 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8101 (mt-10) REVERT: Q 376 GLN cc_start: 0.7835 (tp40) cc_final: 0.7562 (pt0) REVERT: U 176 ARG cc_start: 0.7503 (mtt180) cc_final: 0.6602 (mmt-90) REVERT: U 218 GLN cc_start: 0.8739 (tm-30) cc_final: 0.8534 (tm-30) REVERT: U 251 LYS cc_start: 0.9068 (mmmt) cc_final: 0.8804 (mmmt) REVERT: U 285 ASP cc_start: 0.8980 (t70) cc_final: 0.8655 (t0) REVERT: U 286 ASP cc_start: 0.8548 (t0) cc_final: 0.7851 (p0) REVERT: U 299 MET cc_start: 0.8552 (mmm) cc_final: 0.8040 (mmm) REVERT: Z 62 LYS cc_start: 0.8094 (tttt) cc_final: 0.7504 (mtmt) outliers start: 34 outliers final: 27 residues processed: 261 average time/residue: 0.1413 time to fit residues: 50.8776 Evaluate side-chains 250 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 94 ASN Chi-restraints excluded: chain L residue 160 GLN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 223 LEU Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 274 LYS Chi-restraints excluded: chain Q residue 299 VAL Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain Q residue 381 SER Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain Y residue 113 LEU Chi-restraints excluded: chain Z residue 103 GLN Chi-restraints excluded: chain Z residue 126 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 110 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 126 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 360 ASN U 310 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.152389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111479 restraints weight = 18811.662| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.16 r_work: 0.3124 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13698 Z= 0.140 Angle : 0.522 9.026 18533 Z= 0.269 Chirality : 0.040 0.166 2221 Planarity : 0.003 0.037 2336 Dihedral : 4.095 22.274 1890 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.25 % Favored : 94.63 % Rotamer: Outliers : 2.93 % Allowed : 21.07 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.21), residues: 1733 helix: 1.87 (0.18), residues: 939 sheet: -1.30 (0.34), residues: 236 loop : -2.10 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 74 TYR 0.012 0.001 TYR Y 193 PHE 0.016 0.001 PHE O 178 TRP 0.012 0.001 TRP L 102 HIS 0.003 0.001 HIS U 237 Details of bonding type rmsd covalent geometry : bond 0.00329 (13698) covalent geometry : angle 0.52240 (18533) hydrogen bonds : bond 0.03882 ( 781) hydrogen bonds : angle 3.94586 ( 2334) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: L 34 ASP cc_start: 0.7517 (p0) cc_final: 0.7271 (p0) REVERT: L 160 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8046 (pp30) REVERT: N 255 MET cc_start: 0.9040 (mmm) cc_final: 0.8750 (mmm) REVERT: N 330 MET cc_start: 0.9288 (tpp) cc_final: 0.8967 (tpt) REVERT: O 252 ASP cc_start: 0.8787 (t0) cc_final: 0.8377 (t0) REVERT: O 323 GLU cc_start: 0.8259 (pt0) cc_final: 0.8034 (pt0) REVERT: P 150 MET cc_start: 0.8766 (tpp) cc_final: 0.8441 (mmt) REVERT: P 318 MET cc_start: 0.8809 (ptm) cc_final: 0.8583 (ptt) REVERT: P 348 TYR cc_start: 0.8579 (m-10) cc_final: 0.8353 (m-80) REVERT: Q 266 GLN cc_start: 0.8421 (tp40) cc_final: 0.8048 (mm-40) REVERT: Q 271 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7969 (mt-10) REVERT: Q 376 GLN cc_start: 0.7828 (tp40) cc_final: 0.7560 (pt0) REVERT: U 176 ARG cc_start: 0.7434 (mtt180) cc_final: 0.6602 (mmt-90) REVERT: U 218 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8520 (tm-30) REVERT: U 251 LYS cc_start: 0.9060 (mmmt) cc_final: 0.8801 (mmmt) REVERT: U 285 ASP cc_start: 0.8961 (t70) cc_final: 0.8661 (t0) REVERT: U 299 MET cc_start: 0.8571 (mmm) cc_final: 0.8095 (mmm) REVERT: Y 120 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7610 (pp) REVERT: Z 62 LYS cc_start: 0.8096 (tttt) cc_final: 0.7511 (mtmt) outliers start: 40 outliers final: 31 residues processed: 258 average time/residue: 0.1410 time to fit residues: 50.3856 Evaluate side-chains 258 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 94 ASN Chi-restraints excluded: chain L residue 160 GLN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 223 LEU Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 274 LYS Chi-restraints excluded: chain Q residue 281 THR Chi-restraints excluded: chain Q residue 299 VAL Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain Q residue 381 SER Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain Y residue 113 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 140 LEU Chi-restraints excluded: chain Z residue 20 ILE Chi-restraints excluded: chain Z residue 103 GLN Chi-restraints excluded: chain Z residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.0570 chunk 150 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 58 optimal weight: 0.0770 chunk 4 optimal weight: 6.9990 chunk 144 optimal weight: 0.1980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 360 ASN U 310 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.154499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.113850 restraints weight = 18733.143| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.12 r_work: 0.3154 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13698 Z= 0.103 Angle : 0.499 9.268 18533 Z= 0.257 Chirality : 0.039 0.157 2221 Planarity : 0.003 0.039 2336 Dihedral : 3.929 20.715 1890 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.21 % Favored : 95.67 % Rotamer: Outliers : 2.63 % Allowed : 21.43 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.21), residues: 1733 helix: 2.05 (0.18), residues: 934 sheet: -1.13 (0.34), residues: 236 loop : -2.05 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 74 TYR 0.013 0.001 TYR Y 193 PHE 0.011 0.001 PHE O 178 TRP 0.013 0.001 TRP L 102 HIS 0.003 0.000 HIS U 237 Details of bonding type rmsd covalent geometry : bond 0.00224 (13698) covalent geometry : angle 0.49858 (18533) hydrogen bonds : bond 0.03652 ( 781) hydrogen bonds : angle 3.85279 ( 2334) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 0.559 Fit side-chains REVERT: L 34 ASP cc_start: 0.7533 (p0) cc_final: 0.7253 (p0) REVERT: L 160 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7999 (pp30) REVERT: N 255 MET cc_start: 0.8973 (mmm) cc_final: 0.8735 (mmm) REVERT: O 252 ASP cc_start: 0.8754 (t0) cc_final: 0.8409 (t0) REVERT: O 323 GLU cc_start: 0.8220 (pt0) cc_final: 0.8011 (pt0) REVERT: P 318 MET cc_start: 0.8821 (ptm) cc_final: 0.8578 (ptt) REVERT: Q 266 GLN cc_start: 0.8403 (tp40) cc_final: 0.8032 (mm-40) REVERT: Q 271 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7952 (mt-10) REVERT: Q 364 THR cc_start: 0.9071 (m) cc_final: 0.8852 (p) REVERT: Q 376 GLN cc_start: 0.7757 (tp40) cc_final: 0.7471 (pt0) REVERT: U 176 ARG cc_start: 0.7481 (mtt180) cc_final: 0.6562 (mmt-90) REVERT: U 285 ASP cc_start: 0.8955 (t70) cc_final: 0.8625 (t0) REVERT: U 286 ASP cc_start: 0.8539 (t0) cc_final: 0.7829 (p0) REVERT: U 299 MET cc_start: 0.8584 (mmm) cc_final: 0.8133 (mmm) REVERT: Y 120 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7352 (pp) REVERT: Z 43 TYR cc_start: 0.6448 (p90) cc_final: 0.6242 (p90) REVERT: Z 62 LYS cc_start: 0.8064 (tttt) cc_final: 0.7379 (mtmt) outliers start: 36 outliers final: 28 residues processed: 259 average time/residue: 0.1408 time to fit residues: 50.5571 Evaluate side-chains 256 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 160 GLN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 223 LEU Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 274 LYS Chi-restraints excluded: chain Q residue 299 VAL Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain Q residue 381 SER Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain Y residue 113 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Z residue 20 ILE Chi-restraints excluded: chain Z residue 126 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 15 optimal weight: 0.0040 chunk 57 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 159 optimal weight: 20.0000 chunk 163 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 220 HIS O 360 ASN U 310 ASN Y 99 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.153258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114445 restraints weight = 18561.598| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.04 r_work: 0.3122 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13698 Z= 0.132 Angle : 0.517 8.892 18533 Z= 0.268 Chirality : 0.040 0.152 2221 Planarity : 0.003 0.039 2336 Dihedral : 3.957 20.983 1890 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.79 % Favored : 95.10 % Rotamer: Outliers : 2.78 % Allowed : 21.51 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.21), residues: 1733 helix: 2.08 (0.18), residues: 936 sheet: -1.02 (0.34), residues: 236 loop : -2.00 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 74 TYR 0.011 0.001 TYR P 348 PHE 0.015 0.001 PHE O 178 TRP 0.011 0.001 TRP L 102 HIS 0.003 0.001 HIS U 237 Details of bonding type rmsd covalent geometry : bond 0.00310 (13698) covalent geometry : angle 0.51719 (18533) hydrogen bonds : bond 0.03772 ( 781) hydrogen bonds : angle 3.85471 ( 2334) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 228 time to evaluate : 0.450 Fit side-chains REVERT: L 34 ASP cc_start: 0.7606 (p0) cc_final: 0.7356 (p0) REVERT: N 255 MET cc_start: 0.9023 (mmm) cc_final: 0.8732 (mmm) REVERT: N 330 MET cc_start: 0.9284 (tpp) cc_final: 0.8972 (tpt) REVERT: O 252 ASP cc_start: 0.8818 (t0) cc_final: 0.8396 (t0) REVERT: P 318 MET cc_start: 0.8853 (ptm) cc_final: 0.8621 (ptt) REVERT: P 348 TYR cc_start: 0.8536 (m-80) cc_final: 0.8262 (m-10) REVERT: Q 266 GLN cc_start: 0.8411 (tp40) cc_final: 0.8052 (mm-40) REVERT: Q 271 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7992 (mt-10) REVERT: Q 364 THR cc_start: 0.8961 (m) cc_final: 0.8721 (p) REVERT: Q 376 GLN cc_start: 0.7754 (tp40) cc_final: 0.7484 (pt0) REVERT: U 176 ARG cc_start: 0.7505 (mtt180) cc_final: 0.6640 (mmt-90) REVERT: U 285 ASP cc_start: 0.8958 (t70) cc_final: 0.8645 (t0) REVERT: U 286 ASP cc_start: 0.8568 (t0) cc_final: 0.7846 (p0) REVERT: U 292 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8350 (mm) REVERT: U 299 MET cc_start: 0.8607 (mmm) cc_final: 0.8183 (mmm) REVERT: Y 120 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7376 (pp) REVERT: Y 197 TYR cc_start: 0.8612 (t80) cc_final: 0.8145 (t80) REVERT: Z 62 LYS cc_start: 0.8100 (tttt) cc_final: 0.7405 (mtmt) outliers start: 38 outliers final: 29 residues processed: 254 average time/residue: 0.1400 time to fit residues: 49.2322 Evaluate side-chains 254 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 223 LEU Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 274 LYS Chi-restraints excluded: chain Q residue 299 VAL Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain Q residue 381 SER Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 292 ILE Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain Y residue 113 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 140 LEU Chi-restraints excluded: chain Z residue 20 ILE Chi-restraints excluded: chain Z residue 126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 129 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 145 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 360 ASN Y 99 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.152133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.111668 restraints weight = 18873.981| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.08 r_work: 0.3123 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13698 Z= 0.156 Angle : 0.542 8.959 18533 Z= 0.281 Chirality : 0.041 0.151 2221 Planarity : 0.003 0.044 2336 Dihedral : 4.061 21.856 1890 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.67 % Favored : 95.27 % Rotamer: Outliers : 2.56 % Allowed : 21.73 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.21), residues: 1733 helix: 2.10 (0.18), residues: 936 sheet: -0.98 (0.34), residues: 236 loop : -2.00 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 74 TYR 0.021 0.001 TYR L 3 PHE 0.017 0.001 PHE O 178 TRP 0.010 0.001 TRP L 102 HIS 0.003 0.001 HIS N 213 Details of bonding type rmsd covalent geometry : bond 0.00372 (13698) covalent geometry : angle 0.54180 (18533) hydrogen bonds : bond 0.03929 ( 781) hydrogen bonds : angle 3.92559 ( 2334) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 227 time to evaluate : 0.527 Fit side-chains REVERT: L 34 ASP cc_start: 0.7333 (p0) cc_final: 0.7066 (p0) REVERT: N 330 MET cc_start: 0.9287 (tpp) cc_final: 0.8943 (tpt) REVERT: O 252 ASP cc_start: 0.8797 (t0) cc_final: 0.8380 (t0) REVERT: P 150 MET cc_start: 0.8734 (tpp) cc_final: 0.8398 (mmt) REVERT: P 207 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.7579 (t80) REVERT: P 318 MET cc_start: 0.8817 (ptm) cc_final: 0.8577 (ptt) REVERT: P 348 TYR cc_start: 0.8551 (m-80) cc_final: 0.8192 (m-80) REVERT: Q 266 GLN cc_start: 0.8436 (tp40) cc_final: 0.8062 (mm-40) REVERT: Q 271 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7949 (mt-10) REVERT: Q 364 THR cc_start: 0.8895 (m) cc_final: 0.8650 (p) REVERT: Q 376 GLN cc_start: 0.7738 (tp40) cc_final: 0.7497 (pt0) REVERT: U 176 ARG cc_start: 0.7587 (mtt180) cc_final: 0.6671 (mmt-90) REVERT: U 285 ASP cc_start: 0.8944 (t70) cc_final: 0.8608 (t0) REVERT: U 286 ASP cc_start: 0.8541 (t0) cc_final: 0.7826 (p0) REVERT: U 299 MET cc_start: 0.8603 (mmm) cc_final: 0.8162 (mmm) REVERT: Y 120 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7383 (pp) REVERT: Z 62 LYS cc_start: 0.8111 (tttt) cc_final: 0.7444 (mtmt) outliers start: 35 outliers final: 29 residues processed: 253 average time/residue: 0.1427 time to fit residues: 49.8584 Evaluate side-chains 254 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 223 LEU Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 274 LYS Chi-restraints excluded: chain Q residue 299 VAL Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain Y residue 113 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 140 LEU Chi-restraints excluded: chain Z residue 20 ILE Chi-restraints excluded: chain Z residue 103 GLN Chi-restraints excluded: chain Z residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 29 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 360 ASN Y 99 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111359 restraints weight = 18693.486| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.95 r_work: 0.3125 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13698 Z= 0.171 Angle : 0.557 9.428 18533 Z= 0.289 Chirality : 0.041 0.150 2221 Planarity : 0.003 0.047 2336 Dihedral : 4.120 24.243 1890 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.02 % Favored : 94.92 % Rotamer: Outliers : 2.49 % Allowed : 22.02 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.21), residues: 1733 helix: 2.09 (0.18), residues: 931 sheet: -0.94 (0.34), residues: 236 loop : -1.98 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 74 TYR 0.023 0.001 TYR L 3 PHE 0.023 0.001 PHE L 161 TRP 0.011 0.001 TRP L 112 HIS 0.003 0.001 HIS N 213 Details of bonding type rmsd covalent geometry : bond 0.00411 (13698) covalent geometry : angle 0.55698 (18533) hydrogen bonds : bond 0.04007 ( 781) hydrogen bonds : angle 3.96936 ( 2334) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 34 ASP cc_start: 0.7323 (p0) cc_final: 0.7106 (p0) REVERT: N 255 MET cc_start: 0.8972 (mmm) cc_final: 0.8698 (mmm) REVERT: N 330 MET cc_start: 0.9306 (tpp) cc_final: 0.8968 (tpt) REVERT: O 252 ASP cc_start: 0.8790 (t0) cc_final: 0.8371 (t0) REVERT: P 150 MET cc_start: 0.8718 (tpp) cc_final: 0.8374 (mmt) REVERT: P 207 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7627 (t80) REVERT: P 318 MET cc_start: 0.8808 (ptm) cc_final: 0.8544 (ptt) REVERT: P 348 TYR cc_start: 0.8525 (m-80) cc_final: 0.8174 (m-80) REVERT: Q 266 GLN cc_start: 0.8432 (tp40) cc_final: 0.8053 (mm-40) REVERT: Q 271 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7947 (mt-10) REVERT: Q 364 THR cc_start: 0.8959 (m) cc_final: 0.8707 (p) REVERT: Q 376 GLN cc_start: 0.7761 (tp40) cc_final: 0.7515 (pt0) REVERT: U 176 ARG cc_start: 0.7592 (mtt180) cc_final: 0.6679 (mmt-90) REVERT: U 285 ASP cc_start: 0.8952 (t70) cc_final: 0.8595 (t0) REVERT: U 286 ASP cc_start: 0.8588 (t0) cc_final: 0.7924 (p0) REVERT: U 299 MET cc_start: 0.8571 (mmm) cc_final: 0.8140 (mmm) REVERT: Y 120 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7426 (pp) REVERT: Z 62 LYS cc_start: 0.8116 (tttt) cc_final: 0.7523 (mtmt) outliers start: 34 outliers final: 30 residues processed: 255 average time/residue: 0.1274 time to fit residues: 45.2802 Evaluate side-chains 258 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 223 LEU Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 274 LYS Chi-restraints excluded: chain Q residue 281 THR Chi-restraints excluded: chain Q residue 299 VAL Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain Y residue 108 THR Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 140 LEU Chi-restraints excluded: chain Z residue 20 ILE Chi-restraints excluded: chain Z residue 103 GLN Chi-restraints excluded: chain Z residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 94 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 28 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 360 ASN Y 99 ASN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.152245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112044 restraints weight = 18930.924| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.10 r_work: 0.3113 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13698 Z= 0.150 Angle : 0.546 9.131 18533 Z= 0.285 Chirality : 0.041 0.152 2221 Planarity : 0.003 0.045 2336 Dihedral : 4.078 23.760 1890 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.56 % Favored : 95.38 % Rotamer: Outliers : 2.56 % Allowed : 21.87 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.21), residues: 1733 helix: 2.13 (0.18), residues: 930 sheet: -0.87 (0.34), residues: 236 loop : -1.93 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 74 TYR 0.020 0.001 TYR L 3 PHE 0.019 0.001 PHE L 161 TRP 0.011 0.001 TRP L 102 HIS 0.003 0.001 HIS U 237 Details of bonding type rmsd covalent geometry : bond 0.00357 (13698) covalent geometry : angle 0.54649 (18533) hydrogen bonds : bond 0.03943 ( 781) hydrogen bonds : angle 3.93585 ( 2334) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4407.25 seconds wall clock time: 75 minutes 47.90 seconds (4547.90 seconds total)