Starting phenix.real_space_refine on Thu Jul 31 13:19:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qlf_4581/07_2025/6qlf_4581.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qlf_4581/07_2025/6qlf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6qlf_4581/07_2025/6qlf_4581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qlf_4581/07_2025/6qlf_4581.map" model { file = "/net/cci-nas-00/data/ceres_data/6qlf_4581/07_2025/6qlf_4581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qlf_4581/07_2025/6qlf_4581.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 8, 'ARG:plan': 1} 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: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} 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: {'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} 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: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} 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: {'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 11, 'PHE:plan': 3, 'GLU:plan': 6, '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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 15, 'PHE:plan': 1, 'GLU:plan': 16, '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: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 118 Time building chain proxies: 9.13, per 1000 atoms: 0.68 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: 3.37 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.49 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: 3.78 Time building geometry restraints manager: 4.02 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: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 33.270 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.580 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.002 TRP U 236 HIS 0.006 0.001 HIS U 237 PHE 0.020 0.002 PHE L 161 TYR 0.028 0.002 TYR P 156 ARG 0.004 0.000 ARG N 375 Details of bonding type rmsd hydrogen bonds : bond 0.18103 ( 781) hydrogen bonds : angle 7.45452 ( 2334) covalent geometry : bond 0.00472 (13698) covalent geometry : angle 0.82751 (18533) *********************** 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 : 1.539 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: 0.6684 (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: 0.7487 (ptt) REVERT: Q 264 ARG cc_start: 0.8010 (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: 0.7864 (mptt) REVERT: U 251 LYS cc_start: 0.9213 (mmmt) cc_final: 0.8789 (mmmt) REVERT: U 254 LYS cc_start: 0.8384 (ttmt) cc_final: 0.8074 (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: 0.3521 time to fit residues: 148.8270 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 : 1.462 ------------------------------------------------------------------------------- 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 148 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 53 optimal weight: 0.0770 chunk 83 optimal weight: 0.0670 chunk 102 optimal weight: 0.8980 chunk 159 optimal weight: 10.0000 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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 253 ASN U 257 ASN Y 158 GLN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3811 r_free = 0.3811 target = 0.153938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113523 restraints weight = 18659.737| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.19 r_work: 0.3137 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13698 Z= 0.127 Angle : 0.539 10.132 18533 Z= 0.285 Chirality : 0.041 0.208 2221 Planarity : 0.004 0.040 2336 Dihedral : 4.912 58.833 1896 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.19 % Favored : 94.69 % Rotamer: Outliers : 1.83 % Allowed : 13.53 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.19), residues: 1733 helix: 0.15 (0.17), residues: 934 sheet: -2.21 (0.33), residues: 223 loop : -2.69 (0.22), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 102 HIS 0.005 0.001 HIS U 237 PHE 0.014 0.001 PHE O 178 TYR 0.015 0.001 TYR Q 363 ARG 0.006 0.000 ARG N 197 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 781) hydrogen bonds : angle 4.67400 ( 2334) covalent geometry : bond 0.00278 (13698) covalent geometry : angle 0.53940 (18533) *********************** 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 273 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 2.874 Fit side-chains REVERT: L 34 ASP cc_start: 0.7485 (p0) cc_final: 0.7083 (p0) REVERT: L 58 MET cc_start: 0.8613 (tmm) cc_final: 0.8363 (tmm) REVERT: L 107 TYR cc_start: 0.7658 (m-80) cc_final: 0.7105 (m-80) REVERT: L 160 GLN cc_start: 0.8639 (pp30) cc_final: 0.8257 (pt0) REVERT: N 403 LYS cc_start: 0.8503 (ttmm) cc_final: 0.8213 (mttm) REVERT: O 252 ASP cc_start: 0.8538 (t0) cc_final: 0.8074 (t0) REVERT: O 360 ASN cc_start: 0.8566 (m-40) cc_final: 0.8356 (m-40) REVERT: P 318 MET cc_start: 0.8784 (ptm) cc_final: 0.8566 (ptt) REVERT: P 348 TYR cc_start: 0.8540 (m-10) cc_final: 0.8258 (m-80) REVERT: Q 271 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7889 (mt-10) REVERT: Q 376 GLN cc_start: 0.8061 (tp40) cc_final: 0.7771 (pt0) REVERT: U 176 ARG cc_start: 0.7514 (mtt180) cc_final: 0.6625 (mmt-90) REVERT: U 218 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8486 (tm-30) REVERT: U 251 LYS cc_start: 0.9141 (mmmt) cc_final: 0.8807 (mmmt) REVERT: U 285 ASP cc_start: 0.8997 (t70) cc_final: 0.8642 (t0) REVERT: Y 15 GLU cc_start: 0.8524 (tp30) cc_final: 0.8223 (tp30) REVERT: Y 119 LYS cc_start: 0.8312 (ttpp) cc_final: 0.7821 (ttmm) REVERT: Y 122 GLN cc_start: 0.8644 (pt0) cc_final: 0.8425 (pt0) REVERT: Z 52 ARG cc_start: 0.7418 (ttp80) cc_final: 0.7177 (ptm160) REVERT: Z 62 LYS cc_start: 0.8218 (tttt) cc_final: 0.7398 (mtmt) REVERT: Z 102 GLN cc_start: 0.8186 (tp40) cc_final: 0.7981 (tp-100) outliers start: 25 outliers final: 16 residues processed: 264 average time/residue: 0.4285 time to fit residues: 158.0729 Evaluate side-chains 246 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 230 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 94 ASN 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 206 LEU 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 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 305 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 80 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 148 optimal weight: 0.0470 chunk 142 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 274 GLN O 322 ASN Y 158 GLN ** 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 = 0.3815 r_free = 0.3815 target = 0.154092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.115963 restraints weight = 18758.295| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.09 r_work: 0.3119 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2064 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= 0.127 Angle : 0.513 8.794 18533 Z= 0.268 Chirality : 0.040 0.160 2221 Planarity : 0.003 0.038 2336 Dihedral : 4.510 57.447 1894 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.27 % Favored : 95.61 % Rotamer: Outliers : 2.71 % Allowed : 15.73 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.21), residues: 1733 helix: 1.13 (0.18), residues: 935 sheet: -1.75 (0.35), residues: 222 loop : -2.46 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 112 HIS 0.004 0.001 HIS U 237 PHE 0.015 0.001 PHE O 178 TYR 0.014 0.001 TYR Y 193 ARG 0.006 0.000 ARG O 282 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 781) hydrogen bonds : angle 4.22256 ( 2334) covalent geometry : bond 0.00289 (13698) covalent geometry : angle 0.51318 (18533) *********************** 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 275 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 238 time to evaluate : 2.151 Fit side-chains REVERT: L 34 ASP cc_start: 0.7330 (p0) cc_final: 0.7030 (p0) REVERT: L 58 MET cc_start: 0.8461 (tmm) cc_final: 0.8215 (tmm) REVERT: L 155 ASP cc_start: 0.8583 (t0) cc_final: 0.8359 (t0) REVERT: L 160 GLN cc_start: 0.8464 (pp30) cc_final: 0.8184 (pm20) REVERT: N 330 MET cc_start: 0.9236 (tpp) cc_final: 0.8999 (tpt) REVERT: N 403 LYS cc_start: 0.8397 (ttmm) cc_final: 0.8102 (mttm) REVERT: O 252 ASP cc_start: 0.8587 (t0) cc_final: 0.8160 (t0) REVERT: O 360 ASN cc_start: 0.8575 (m-40) cc_final: 0.8373 (m-40) REVERT: P 318 MET cc_start: 0.8577 (ptm) cc_final: 0.8351 (ptt) REVERT: P 348 TYR cc_start: 0.8440 (m-10) cc_final: 0.8189 (m-80) REVERT: Q 270 GLU cc_start: 0.7925 (tp30) cc_final: 0.7352 (tp30) REVERT: Q 271 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8000 (mt-10) REVERT: Q 376 GLN cc_start: 0.7899 (tp40) cc_final: 0.7625 (pt0) REVERT: U 176 ARG cc_start: 0.7488 (mtt180) cc_final: 0.6593 (mmt-90) REVERT: U 251 LYS cc_start: 0.9066 (mmmt) cc_final: 0.8784 (mmmt) REVERT: U 285 ASP cc_start: 0.8898 (t70) cc_final: 0.8573 (t0) REVERT: U 286 ASP cc_start: 0.8388 (t0) cc_final: 0.7773 (p0) REVERT: Y 15 GLU cc_start: 0.8395 (tp30) cc_final: 0.8128 (tp30) REVERT: Z 43 TYR cc_start: 0.6499 (p90) cc_final: 0.4992 (t80) REVERT: Z 52 ARG cc_start: 0.7423 (ttp80) cc_final: 0.7199 (ttp-170) REVERT: Z 62 LYS cc_start: 0.8107 (tttt) cc_final: 0.7462 (mtmt) REVERT: Z 102 GLN cc_start: 0.8098 (tp40) cc_final: 0.7868 (tp-100) outliers start: 37 outliers final: 23 residues processed: 263 average time/residue: 0.4255 time to fit residues: 155.3945 Evaluate side-chains 252 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 5.173 ------------------------------------------------------------------------------- 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 N residue 30 THR Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 424 ILE 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 310 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 58 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 153 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 115 optimal weight: 0.0040 chunk 85 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 158 GLN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.153417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112810 restraints weight = 18573.082| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.07 r_work: 0.3140 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13698 Z= 0.134 Angle : 0.507 8.836 18533 Z= 0.266 Chirality : 0.041 0.256 2221 Planarity : 0.003 0.037 2336 Dihedral : 4.360 51.086 1892 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.85 % Favored : 95.04 % Rotamer: Outliers : 2.71 % Allowed : 17.04 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.21), residues: 1733 helix: 1.53 (0.18), residues: 936 sheet: -1.47 (0.34), residues: 230 loop : -2.32 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 102 HIS 0.004 0.001 HIS U 237 PHE 0.016 0.001 PHE O 178 TYR 0.010 0.001 TYR Y 193 ARG 0.007 0.000 ARG N 74 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 781) hydrogen bonds : angle 4.07936 ( 2334) covalent geometry : bond 0.00312 (13698) covalent geometry : angle 0.50717 (18533) *********************** 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 271 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 2.620 Fit side-chains revert: symmetry clash REVERT: L 34 ASP cc_start: 0.7543 (p0) cc_final: 0.7262 (p0) REVERT: L 155 ASP cc_start: 0.8833 (t0) cc_final: 0.8600 (t0) REVERT: L 160 GLN cc_start: 0.8619 (pp30) cc_final: 0.8392 (pm20) REVERT: N 330 MET cc_start: 0.9298 (tpp) cc_final: 0.9027 (tpt) REVERT: O 252 ASP cc_start: 0.8701 (t0) cc_final: 0.8333 (t0) REVERT: O 323 GLU cc_start: 0.8268 (pt0) cc_final: 0.8007 (pt0) REVERT: P 318 MET cc_start: 0.8773 (ptm) cc_final: 0.8556 (ptt) REVERT: P 348 TYR cc_start: 0.8473 (m-10) cc_final: 0.8233 (m-80) REVERT: Q 270 GLU cc_start: 0.8137 (tp30) cc_final: 0.7502 (tp30) REVERT: Q 271 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8041 (mt-10) REVERT: Q 376 GLN cc_start: 0.7861 (tp40) cc_final: 0.7655 (pt0) REVERT: U 176 ARG cc_start: 0.7479 (mtt180) cc_final: 0.6627 (mmt-90) REVERT: U 251 LYS cc_start: 0.9097 (mmmt) cc_final: 0.8819 (mmmt) REVERT: U 285 ASP cc_start: 0.8979 (t70) cc_final: 0.8647 (t0) REVERT: Y 13 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7646 (mt-10) REVERT: Y 15 GLU cc_start: 0.8459 (tp30) cc_final: 0.8154 (tp30) REVERT: Y 120 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7655 (pp) REVERT: Z 43 TYR cc_start: 0.6544 (p90) cc_final: 0.4462 (m-80) REVERT: Z 52 ARG cc_start: 0.7453 (ttp80) cc_final: 0.7253 (ttp-170) REVERT: Z 62 LYS cc_start: 0.8144 (tttt) cc_final: 0.7510 (mtmt) outliers start: 37 outliers final: 26 residues processed: 258 average time/residue: 0.4323 time to fit residues: 156.1427 Evaluate side-chains 243 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 1.930 ------------------------------------------------------------------------------- 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 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 424 ILE Chi-restraints excluded: chain O residue 202 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 Z residue 20 ILE 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 162 optimal weight: 4.9990 chunk 8 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 60 optimal weight: 0.0570 chunk 59 optimal weight: 0.3980 chunk 141 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 310 ASN Y 158 GLN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.154427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113410 restraints weight = 18789.804| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.06 r_work: 0.3164 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13698 Z= 0.110 Angle : 0.489 10.604 18533 Z= 0.255 Chirality : 0.040 0.195 2221 Planarity : 0.003 0.039 2336 Dihedral : 4.127 41.549 1892 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.56 % Favored : 95.33 % Rotamer: Outliers : 2.41 % Allowed : 18.14 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1733 helix: 1.81 (0.18), residues: 937 sheet: -1.33 (0.34), residues: 230 loop : -2.17 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 102 HIS 0.003 0.001 HIS U 237 PHE 0.013 0.001 PHE O 178 TYR 0.010 0.001 TYR Y 193 ARG 0.007 0.000 ARG N 74 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 781) hydrogen bonds : angle 3.91156 ( 2334) covalent geometry : bond 0.00245 (13698) covalent geometry : angle 0.48898 (18533) *********************** 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 264 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 4.561 Fit side-chains revert: symmetry clash REVERT: L 34 ASP cc_start: 0.7491 (p0) cc_final: 0.7230 (p0) REVERT: L 155 ASP cc_start: 0.8757 (t0) cc_final: 0.8480 (t0) REVERT: L 160 GLN cc_start: 0.8582 (pp30) cc_final: 0.8252 (pm20) REVERT: O 252 ASP cc_start: 0.8694 (t0) cc_final: 0.8339 (t0) REVERT: O 323 GLU cc_start: 0.8265 (pt0) cc_final: 0.8025 (pt0) REVERT: P 270 ARG cc_start: 0.8139 (mtt-85) cc_final: 0.7908 (tpt-90) REVERT: P 318 MET cc_start: 0.8759 (ptm) cc_final: 0.8533 (ptt) REVERT: Q 271 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7904 (mt-10) REVERT: Q 376 GLN cc_start: 0.7877 (tp40) cc_final: 0.7599 (pt0) REVERT: U 176 ARG cc_start: 0.7449 (mtt180) cc_final: 0.6580 (mmt-90) REVERT: U 251 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8794 (mmmt) REVERT: U 285 ASP cc_start: 0.8971 (t70) cc_final: 0.8636 (t0) REVERT: U 299 MET cc_start: 0.8533 (mmm) cc_final: 0.8038 (mmm) REVERT: U 308 LYS cc_start: 0.8100 (mmtp) cc_final: 0.7280 (tttt) REVERT: Y 120 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7486 (pp) REVERT: Z 43 TYR cc_start: 0.6491 (p90) cc_final: 0.4536 (m-80) REVERT: Z 62 LYS cc_start: 0.8050 (tttt) cc_final: 0.7380 (mtmt) outliers start: 33 outliers final: 27 residues processed: 255 average time/residue: 0.4918 time to fit residues: 174.8737 Evaluate side-chains 247 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 1.783 ------------------------------------------------------------------------------- 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 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 424 ILE Chi-restraints excluded: chain O residue 197 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 120 LEU Chi-restraints excluded: chain Z residue 20 ILE Chi-restraints excluded: chain Z residue 103 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 173 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 109 optimal weight: 0.0970 chunk 54 optimal weight: 0.0980 chunk 162 optimal weight: 2.9990 chunk 76 optimal weight: 0.1980 chunk 57 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 252 HIS ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 158 GLN ** 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 = 0.3829 r_free = 0.3829 target = 0.155316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114780 restraints weight = 18907.091| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.18 r_work: 0.3150 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13698 Z= 0.107 Angle : 0.490 9.252 18533 Z= 0.254 Chirality : 0.039 0.173 2221 Planarity : 0.003 0.036 2336 Dihedral : 3.957 30.985 1892 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.56 % Favored : 95.33 % Rotamer: Outliers : 2.63 % Allowed : 18.87 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1733 helix: 2.02 (0.18), residues: 934 sheet: -1.22 (0.34), residues: 235 loop : -2.06 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 102 HIS 0.003 0.000 HIS U 237 PHE 0.013 0.001 PHE O 178 TYR 0.011 0.001 TYR Y 193 ARG 0.008 0.000 ARG N 74 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 781) hydrogen bonds : angle 3.82876 ( 2334) covalent geometry : bond 0.00237 (13698) covalent geometry : angle 0.48997 (18533) *********************** 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 266 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 1.774 Fit side-chains REVERT: L 34 ASP cc_start: 0.7567 (p0) cc_final: 0.7307 (p0) REVERT: L 95 ARG cc_start: 0.7948 (mtm-85) cc_final: 0.7657 (ttm170) REVERT: L 155 ASP cc_start: 0.8827 (t0) cc_final: 0.8539 (t0) REVERT: L 160 GLN cc_start: 0.8602 (pp30) cc_final: 0.8385 (pm20) REVERT: O 252 ASP cc_start: 0.8725 (t0) cc_final: 0.8361 (t0) REVERT: P 270 ARG cc_start: 0.8221 (mtt-85) cc_final: 0.7881 (tpt-90) REVERT: P 318 MET cc_start: 0.8821 (ptm) cc_final: 0.8598 (ptt) REVERT: P 348 TYR cc_start: 0.8522 (m-80) cc_final: 0.8253 (m-80) REVERT: Q 271 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7916 (mt-10) REVERT: Q 376 GLN cc_start: 0.7821 (tp40) cc_final: 0.7543 (pt0) REVERT: U 176 ARG cc_start: 0.7467 (mtt180) cc_final: 0.6567 (mmt-90) REVERT: U 285 ASP cc_start: 0.8837 (t70) cc_final: 0.8561 (t0) REVERT: U 299 MET cc_start: 0.8609 (mmm) cc_final: 0.8130 (mmm) REVERT: U 308 LYS cc_start: 0.8029 (mmtp) cc_final: 0.7209 (tttt) REVERT: Y 120 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7277 (pp) REVERT: Z 43 TYR cc_start: 0.6413 (p90) cc_final: 0.4578 (m-80) REVERT: Z 62 LYS cc_start: 0.8033 (tttt) cc_final: 0.7342 (mtmt) REVERT: Z 113 GLN cc_start: 0.8235 (tp-100) cc_final: 0.7956 (mt0) outliers start: 36 outliers final: 28 residues processed: 255 average time/residue: 0.3483 time to fit residues: 125.6503 Evaluate side-chains 249 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 1.624 ------------------------------------------------------------------------------- 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 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 N residue 424 ILE 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 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 57 LEU Chi-restraints excluded: chain Z residue 103 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 127 optimal weight: 1.9990 chunk 36 optimal weight: 0.0270 chunk 22 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 143 optimal weight: 0.0370 chunk 160 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 220 HIS Y 158 GLN ** 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 = 0.151887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110885 restraints weight = 18860.298| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.10 r_work: 0.3117 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2624 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= 0.173 Angle : 0.544 10.286 18533 Z= 0.279 Chirality : 0.041 0.156 2221 Planarity : 0.003 0.043 2336 Dihedral : 4.075 21.845 1890 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.08 % Favored : 94.81 % Rotamer: Outliers : 3.00 % Allowed : 19.24 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1733 helix: 1.99 (0.18), residues: 936 sheet: -1.10 (0.34), residues: 236 loop : -1.99 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 112 HIS 0.003 0.001 HIS N 213 PHE 0.019 0.001 PHE O 178 TYR 0.013 0.001 TYR Y 193 ARG 0.009 0.000 ARG Z 104 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 781) hydrogen bonds : angle 3.92742 ( 2334) covalent geometry : bond 0.00416 (13698) covalent geometry : angle 0.54446 (18533) *********************** 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 261 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 220 time to evaluate : 1.576 Fit side-chains REVERT: L 34 ASP cc_start: 0.7473 (p0) cc_final: 0.7197 (p0) REVERT: L 95 ARG cc_start: 0.7948 (mtm-85) cc_final: 0.7735 (ttm170) REVERT: L 155 ASP cc_start: 0.8870 (t0) cc_final: 0.8617 (t0) REVERT: L 160 GLN cc_start: 0.8613 (pp30) cc_final: 0.8392 (pm20) REVERT: N 255 MET cc_start: 0.9135 (mmm) cc_final: 0.8862 (mmm) REVERT: N 330 MET cc_start: 0.9301 (tpp) cc_final: 0.8985 (tpt) REVERT: O 252 ASP cc_start: 0.8790 (t0) cc_final: 0.8351 (t0) REVERT: P 318 MET cc_start: 0.8796 (ptm) cc_final: 0.8561 (ptt) REVERT: P 348 TYR cc_start: 0.8593 (m-80) cc_final: 0.8250 (m-80) REVERT: Q 271 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7895 (mt-10) REVERT: Q 376 GLN cc_start: 0.7756 (tp40) cc_final: 0.7479 (pt0) REVERT: U 176 ARG cc_start: 0.7551 (mtt180) cc_final: 0.6585 (mmt-90) REVERT: U 255 ARG cc_start: 0.8063 (mmt-90) cc_final: 0.7826 (mtt180) REVERT: U 285 ASP cc_start: 0.8790 (t70) cc_final: 0.8564 (t0) REVERT: U 299 MET cc_start: 0.8590 (mmm) cc_final: 0.8129 (mmm) REVERT: U 308 LYS cc_start: 0.8074 (mmtp) cc_final: 0.7228 (tttt) REVERT: Y 120 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7459 (pp) REVERT: Z 43 TYR cc_start: 0.6466 (p90) cc_final: 0.4522 (m-80) REVERT: Z 62 LYS cc_start: 0.8103 (tttt) cc_final: 0.7403 (mtmt) outliers start: 41 outliers final: 32 residues processed: 246 average time/residue: 0.3036 time to fit residues: 103.7201 Evaluate side-chains 248 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 94 ASN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 97 MET 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 N residue 424 ILE 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 228 GLN Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Z residue 20 ILE Chi-restraints excluded: chain Z residue 53 VAL 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 97 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 122 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 158 GLN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.152441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112325 restraints weight = 18812.057| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.20 r_work: 0.3106 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13698 Z= 0.145 Angle : 0.534 11.317 18533 Z= 0.273 Chirality : 0.041 0.154 2221 Planarity : 0.003 0.038 2336 Dihedral : 4.041 21.850 1890 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.56 % Favored : 95.38 % Rotamer: Outliers : 2.63 % Allowed : 20.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1733 helix: 2.06 (0.18), residues: 936 sheet: -1.04 (0.34), residues: 236 loop : -1.96 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 102 HIS 0.003 0.001 HIS U 237 PHE 0.016 0.001 PHE O 178 TYR 0.014 0.001 TYR Y 193 ARG 0.007 0.000 ARG N 74 Details of bonding type rmsd hydrogen bonds : bond 0.03877 ( 781) hydrogen bonds : angle 3.89879 ( 2334) covalent geometry : bond 0.00341 (13698) covalent geometry : angle 0.53380 (18533) *********************** 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 260 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 224 time to evaluate : 1.484 Fit side-chains revert: symmetry clash REVERT: L 34 ASP cc_start: 0.7446 (p0) cc_final: 0.7187 (p0) REVERT: L 155 ASP cc_start: 0.8912 (t0) cc_final: 0.8655 (t0) REVERT: L 160 GLN cc_start: 0.8634 (pp30) cc_final: 0.8433 (pm20) REVERT: N 330 MET cc_start: 0.9288 (tpp) cc_final: 0.8965 (tpt) REVERT: O 231 ASN cc_start: 0.8579 (t0) cc_final: 0.8374 (t0) REVERT: O 252 ASP cc_start: 0.8805 (t0) cc_final: 0.8363 (t0) REVERT: P 318 MET cc_start: 0.8864 (ptm) cc_final: 0.8616 (ptt) REVERT: P 348 TYR cc_start: 0.8585 (m-80) cc_final: 0.8306 (m-10) REVERT: Q 271 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7956 (mt-10) REVERT: Q 376 GLN cc_start: 0.7749 (tp40) cc_final: 0.7483 (pt0) REVERT: U 176 ARG cc_start: 0.7478 (mtt180) cc_final: 0.6602 (mmt-90) REVERT: U 285 ASP cc_start: 0.8923 (t70) cc_final: 0.8657 (t0) REVERT: U 299 MET cc_start: 0.8676 (mmm) cc_final: 0.8165 (mmm) REVERT: U 308 LYS cc_start: 0.8075 (mmtp) cc_final: 0.7244 (tttt) REVERT: Y 120 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7427 (pp) REVERT: Z 43 TYR cc_start: 0.6416 (p90) cc_final: 0.4565 (m-80) REVERT: Z 62 LYS cc_start: 0.8079 (tttt) cc_final: 0.7381 (mtmt) outliers start: 36 outliers final: 29 residues processed: 250 average time/residue: 0.3098 time to fit residues: 106.6582 Evaluate side-chains 250 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 94 ASN 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 N residue 399 THR Chi-restraints excluded: chain N residue 424 ILE 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 U residue 220 ILE Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Z residue 20 ILE Chi-restraints excluded: chain Z residue 85 LEU Chi-restraints excluded: chain Z residue 103 GLN 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 110 optimal weight: 1.9990 chunk 154 optimal weight: 0.5980 chunk 71 optimal weight: 0.0020 chunk 31 optimal weight: 0.7980 chunk 104 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 99 ASN Y 158 GLN ** 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 = 0.3812 r_free = 0.3812 target = 0.153867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113358 restraints weight = 18768.916| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.10 r_work: 0.3147 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 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 : 0.003 0.032 13698 Z= 0.120 Angle : 0.523 11.605 18533 Z= 0.267 Chirality : 0.040 0.156 2221 Planarity : 0.003 0.036 2336 Dihedral : 3.906 20.636 1890 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.56 % Favored : 95.38 % Rotamer: Outliers : 2.19 % Allowed : 21.07 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.21), residues: 1733 helix: 2.20 (0.18), residues: 935 sheet: -1.04 (0.34), residues: 241 loop : -1.90 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 102 HIS 0.003 0.001 HIS U 237 PHE 0.014 0.001 PHE O 178 TYR 0.011 0.001 TYR Y 193 ARG 0.008 0.000 ARG N 74 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 781) hydrogen bonds : angle 3.80777 ( 2334) covalent geometry : bond 0.00275 (13698) covalent geometry : angle 0.52318 (18533) *********************** 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 250 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 1.577 Fit side-chains REVERT: L 34 ASP cc_start: 0.7453 (p0) cc_final: 0.7158 (p0) REVERT: L 155 ASP cc_start: 0.8849 (t0) cc_final: 0.8599 (t0) REVERT: O 252 ASP cc_start: 0.8752 (t0) cc_final: 0.8326 (t0) REVERT: O 295 HIS cc_start: 0.7709 (m-70) cc_final: 0.7395 (m-70) REVERT: P 318 MET cc_start: 0.8825 (ptm) cc_final: 0.8572 (ptt) REVERT: P 348 TYR cc_start: 0.8515 (m-80) cc_final: 0.8259 (m-10) REVERT: Q 271 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7915 (mt-10) REVERT: Q 376 GLN cc_start: 0.7750 (tp40) cc_final: 0.7473 (pt0) REVERT: U 176 ARG cc_start: 0.7475 (mtt180) cc_final: 0.6592 (mmt-90) REVERT: U 285 ASP cc_start: 0.8915 (t70) cc_final: 0.8598 (t0) REVERT: U 286 ASP cc_start: 0.8544 (t0) cc_final: 0.7836 (p0) REVERT: Y 120 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7289 (pp) REVERT: Z 43 TYR cc_start: 0.6324 (p90) cc_final: 0.4524 (m-80) outliers start: 30 outliers final: 27 residues processed: 245 average time/residue: 0.2927 time to fit residues: 99.4525 Evaluate side-chains 246 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 N residue 424 ILE 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 U residue 220 ILE Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Z residue 20 ILE Chi-restraints excluded: chain Z residue 103 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 102 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 chunk 169 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 99 ASN Y 158 GLN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 83 HIS Z 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.152821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112100 restraints weight = 18749.612| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.11 r_work: 0.3121 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13698 Z= 0.152 Angle : 0.552 11.934 18533 Z= 0.282 Chirality : 0.041 0.152 2221 Planarity : 0.003 0.047 2336 Dihedral : 4.016 21.364 1890 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.85 % Favored : 95.10 % Rotamer: Outliers : 2.12 % Allowed : 21.29 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1733 helix: 2.18 (0.18), residues: 936 sheet: -1.02 (0.34), residues: 241 loop : -1.86 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 102 HIS 0.003 0.001 HIS U 237 PHE 0.017 0.001 PHE O 178 TYR 0.022 0.001 TYR N 33 ARG 0.009 0.000 ARG N 74 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 781) hydrogen bonds : angle 3.86396 ( 2334) covalent geometry : bond 0.00362 (13698) covalent geometry : angle 0.55210 (18533) ********************** 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 251 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 1.553 Fit side-chains revert: symmetry clash REVERT: L 34 ASP cc_start: 0.7463 (p0) cc_final: 0.7204 (p0) REVERT: L 155 ASP cc_start: 0.8886 (t0) cc_final: 0.8647 (t0) REVERT: N 330 MET cc_start: 0.9291 (tpp) cc_final: 0.8965 (tpt) REVERT: O 252 ASP cc_start: 0.8799 (t0) cc_final: 0.8364 (t0) REVERT: P 318 MET cc_start: 0.8820 (ptm) cc_final: 0.8574 (ptt) REVERT: P 348 TYR cc_start: 0.8515 (m-80) cc_final: 0.8243 (m-10) REVERT: Q 271 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7928 (mt-10) REVERT: Q 376 GLN cc_start: 0.7779 (tp40) cc_final: 0.7500 (pt0) REVERT: U 176 ARG cc_start: 0.7598 (mtt180) cc_final: 0.6649 (mmt-90) REVERT: U 285 ASP cc_start: 0.8916 (t70) cc_final: 0.8648 (t0) REVERT: Y 120 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7419 (pp) REVERT: Z 43 TYR cc_start: 0.6362 (p90) cc_final: 0.4474 (m-80) REVERT: Z 62 LYS cc_start: 0.8067 (tttt) cc_final: 0.7422 (mtmt) outliers start: 29 outliers final: 28 residues processed: 247 average time/residue: 0.2970 time to fit residues: 102.4444 Evaluate side-chains 249 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 1.580 ------------------------------------------------------------------------------- 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 N residue 424 ILE 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 U residue 220 ILE Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain Y residue 120 LEU Chi-restraints excluded: chain Y residue 181 ILE Chi-restraints excluded: chain Z residue 20 ILE Chi-restraints excluded: chain Z residue 103 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 9 optimal weight: 0.0870 chunk 6 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 125 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 99 ASN Y 158 GLN ** Y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 83 HIS Z 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.153693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.114830 restraints weight = 18772.464| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.00 r_work: 0.3144 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13698 Z= 0.131 Angle : 0.547 11.989 18533 Z= 0.280 Chirality : 0.040 0.155 2221 Planarity : 0.003 0.038 2336 Dihedral : 3.949 22.453 1890 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.61 % Rotamer: Outliers : 2.49 % Allowed : 21.36 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.21), residues: 1733 helix: 2.29 (0.18), residues: 948 sheet: -0.95 (0.34), residues: 240 loop : -1.87 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 102 HIS 0.003 0.001 HIS U 237 PHE 0.014 0.001 PHE O 178 TYR 0.014 0.001 TYR Y 193 ARG 0.008 0.000 ARG N 74 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 781) hydrogen bonds : angle 3.82565 ( 2334) covalent geometry : bond 0.00306 (13698) covalent geometry : angle 0.54722 (18533) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10112.08 seconds wall clock time: 183 minutes 13.71 seconds (10993.71 seconds total)