Starting phenix.real_space_refine on Thu Feb 13 20:28:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lml_0918/02_2025/6lml_0918.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lml_0918/02_2025/6lml_0918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lml_0918/02_2025/6lml_0918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lml_0918/02_2025/6lml_0918.map" model { file = "/net/cci-nas-00/data/ceres_data/6lml_0918/02_2025/6lml_0918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lml_0918/02_2025/6lml_0918.cif" } resolution = 3.9 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 6036 2.51 5 N 1625 2.21 5 O 1718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9438 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1735 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2322 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 300} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 241 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 28} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1742 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 245 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "R" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3153 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N LEU A 234 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 234 " occ=0.00 residue: pdb=" N ALA A 235 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A 235 " occ=0.00 residue: pdb=" N GLU A 236 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 236 " occ=0.00 residue: pdb=" N ASP A 237 " occ=0.00 ... (3 atoms not shown) pdb=" CB ASP A 237 " occ=0.00 residue: pdb=" N GLU A 238 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 238 " occ=0.00 residue: pdb=" N GLU A 239 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 239 " occ=0.00 residue: pdb=" N MET A 240 " occ=0.00 ... (3 atoms not shown) pdb=" CB MET A 240 " occ=0.00 Time building chain proxies: 5.88, per 1000 atoms: 0.62 Number of scatterers: 9438 At special positions: 0 Unit cell: (153.34, 112.34, 109.06, 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 59 16.00 O 1718 8.00 N 1625 7.00 C 6036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " distance=2.03 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.03 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.03 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.2 seconds 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2266 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 19 sheets defined 32.3% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 11 through 30 removed outlier: 4.255A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 4.130A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.517A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.572A pdb=" N MET A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.699A pdb=" N PHE A 259 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 260' Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 295 through 308 removed outlier: 4.738A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N CYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 348 removed outlier: 3.533A pdb=" N THR A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.726A pdb=" N ALA C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.630A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.640A pdb=" N SER D 31 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.596A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'E' and resid 2 through 27 removed outlier: 4.430A pdb=" N SER E 8 " --> pdb=" O GLY E 4 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS E 12 " --> pdb=" O SER E 8 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER E 16 " --> pdb=" O LYS E 12 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 41 removed outlier: 3.511A pdb=" N GLU R 34 " --> pdb=" O ASP R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 Processing helix chain 'R' and resid 118 through 122 removed outlier: 3.632A pdb=" N GLN R 122 " --> pdb=" O SER R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 166 removed outlier: 3.521A pdb=" N ILE R 128 " --> pdb=" O ASP R 124 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL R 134 " --> pdb=" O VAL R 130 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL R 143 " --> pdb=" O SER R 139 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR R 146 " --> pdb=" O GLN R 142 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL R 147 " --> pdb=" O VAL R 143 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU R 158 " --> pdb=" O GLY R 154 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE R 162 " --> pdb=" O LEU R 158 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU R 163 " --> pdb=" O ALA R 159 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU R 166 " --> pdb=" O ILE R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 182 Processing helix chain 'R' and resid 184 through 197 removed outlier: 3.921A pdb=" N SER R 190 " --> pdb=" O LEU R 186 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE R 194 " --> pdb=" O SER R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 216 removed outlier: 3.594A pdb=" N THR R 214 " --> pdb=" O LEU R 210 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU R 216 " --> pdb=" O VAL R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 235 removed outlier: 3.824A pdb=" N ALA R 228 " --> pdb=" O CYS R 224 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL R 229 " --> pdb=" O ARG R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 240 through 253 removed outlier: 3.523A pdb=" N VAL R 244 " --> pdb=" O CYS R 240 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU R 249 " --> pdb=" O GLU R 245 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 272 removed outlier: 3.641A pdb=" N TYR R 267 " --> pdb=" O PHE R 263 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY R 269 " --> pdb=" O SER R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 274 through 277 Processing helix chain 'R' and resid 278 through 288 removed outlier: 3.595A pdb=" N LEU R 288 " --> pdb=" O VAL R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 305 Processing helix chain 'R' and resid 308 through 330 removed outlier: 3.715A pdb=" N ILE R 315 " --> pdb=" O VAL R 311 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU R 316 " --> pdb=" O PHE R 312 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN R 318 " --> pdb=" O ALA R 314 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE R 320 " --> pdb=" O LEU R 316 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE R 325 " --> pdb=" O ILE R 321 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN R 327 " --> pdb=" O VAL R 323 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU R 329 " --> pdb=" O ILE R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 333 No H-bonds generated for 'chain 'R' and resid 331 through 333' Processing helix chain 'R' and resid 334 through 338 removed outlier: 3.776A pdb=" N GLN R 337 " --> pdb=" O ARG R 334 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N MET R 338 " --> pdb=" O ALA R 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 334 through 338' Processing helix chain 'R' and resid 340 through 344 removed outlier: 3.545A pdb=" N TYR R 343 " --> pdb=" O HIS R 340 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS R 344 " --> pdb=" O THR R 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 340 through 344' Processing helix chain 'R' and resid 345 through 350 Processing helix chain 'R' and resid 375 through 403 removed outlier: 3.874A pdb=" N SER R 379 " --> pdb=" O GLY R 375 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU R 382 " --> pdb=" O ARG R 378 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE R 383 " --> pdb=" O SER R 379 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU R 386 " --> pdb=" O LEU R 382 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL R 396 " --> pdb=" O GLN R 392 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR R 400 " --> pdb=" O VAL R 396 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N CYS R 401 " --> pdb=" O ALA R 397 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU R 403 " --> pdb=" O LEU R 399 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 418 removed outlier: 3.586A pdb=" N ARG R 413 " --> pdb=" O SER R 409 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.207A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.592A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 322 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.905A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 113 removed outlier: 6.023A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.894A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.453A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.560A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.523A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 328 through 329 removed outlier: 3.689A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 7 removed outlier: 4.006A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.503A pdb=" N THR D 115 " --> pdb=" O TYR D 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 59 through 60 removed outlier: 4.165A pdb=" N TYR D 50 " --> pdb=" O TYR D 59 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AB6, first strand: chain 'D' and resid 146 through 148 removed outlier: 6.510A pdb=" N VAL D 147 " --> pdb=" O GLU D 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 155 through 159 removed outlier: 3.666A pdb=" N SER D 206 " --> pdb=" O THR D 213 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 177 through 179 Processing sheet with id=AB9, first strand: chain 'D' and resid 189 through 190 Processing sheet with id=AC1, first strand: chain 'R' and resid 79 through 80 removed outlier: 4.097A pdb=" N ILE R 79 " --> pdb=" O VAL R 96 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 2.95 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: 3020 1.34 - 1.46: 2422 1.46 - 1.58: 4144 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 9666 Sorted by residual: bond pdb=" C ILE R 355 " pdb=" N PRO R 356 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.47e+00 bond pdb=" C TRP B 99 " pdb=" N VAL B 100 " ideal model delta sigma weight residual 1.334 1.307 0.027 1.29e-02 6.01e+03 4.49e+00 bond pdb=" N THR R 257 " pdb=" CA THR R 257 " ideal model delta sigma weight residual 1.460 1.485 -0.025 1.54e-02 4.22e+03 2.74e+00 bond pdb=" CB ASN R 238 " pdb=" CG ASN R 238 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.42e+00 bond pdb=" CA ASN R 238 " pdb=" CB ASN R 238 " ideal model delta sigma weight residual 1.534 1.512 0.022 1.45e-02 4.76e+03 2.23e+00 ... (remaining 9661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 12851 2.73 - 5.46: 243 5.46 - 8.18: 27 8.18 - 10.91: 4 10.91 - 13.64: 3 Bond angle restraints: 13128 Sorted by residual: angle pdb=" N VAL R 191 " pdb=" CA VAL R 191 " pdb=" C VAL R 191 " ideal model delta sigma weight residual 112.96 106.65 6.31 1.00e+00 1.00e+00 3.98e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 122.46 129.03 -6.57 1.41e+00 5.03e-01 2.17e+01 angle pdb=" C VAL R 368 " pdb=" N THR R 369 " pdb=" CA THR R 369 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.04e+01 angle pdb=" N VAL R 236 " pdb=" CA VAL R 236 " pdb=" C VAL R 236 " ideal model delta sigma weight residual 113.53 109.12 4.41 9.80e-01 1.04e+00 2.02e+01 angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 ... (remaining 13123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 4893 17.10 - 34.21: 597 34.21 - 51.31: 126 51.31 - 68.41: 13 68.41 - 85.52: 7 Dihedral angle restraints: 5636 sinusoidal: 2115 harmonic: 3521 Sorted by residual: dihedral pdb=" CA PRO R 356 " pdb=" C PRO R 356 " pdb=" N LEU R 357 " pdb=" CA LEU R 357 " ideal model delta harmonic sigma weight residual 180.00 140.63 39.37 0 5.00e+00 4.00e-02 6.20e+01 dihedral pdb=" CA VAL R 292 " pdb=" C VAL R 292 " pdb=" N GLN R 293 " pdb=" CA GLN R 293 " ideal model delta harmonic sigma weight residual 180.00 -144.91 -35.09 0 5.00e+00 4.00e-02 4.93e+01 dihedral pdb=" CA GLY B 77 " pdb=" C GLY B 77 " pdb=" N LYS B 78 " pdb=" CA LYS B 78 " ideal model delta harmonic sigma weight residual -180.00 -151.84 -28.16 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 5633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1128 0.062 - 0.123: 290 0.123 - 0.185: 40 0.185 - 0.246: 6 0.246 - 0.307: 3 Chirality restraints: 1467 Sorted by residual: chirality pdb=" CB VAL R 91 " pdb=" CA VAL R 91 " pdb=" CG1 VAL R 91 " pdb=" CG2 VAL R 91 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB ILE D 100 " pdb=" CA ILE D 100 " pdb=" CG1 ILE D 100 " pdb=" CG2 ILE D 100 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 1464 not shown) Planarity restraints: 1661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.031 2.00e-02 2.50e+03 2.23e-02 9.97e+00 pdb=" CG TYR B 59 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 355 " 0.042 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO R 356 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO R 356 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 356 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 184 " -0.040 5.00e-02 4.00e+02 6.12e-02 5.99e+00 pdb=" N PRO D 185 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO D 185 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 185 " -0.034 5.00e-02 4.00e+02 ... (remaining 1658 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2621 2.79 - 3.32: 8200 3.32 - 3.84: 15594 3.84 - 4.37: 17849 4.37 - 4.90: 30125 Nonbonded interactions: 74389 Sorted by model distance: nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.260 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.270 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.274 3.040 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.276 3.040 nonbonded pdb=" O SER R 183 " pdb=" OG SER R 183 " model vdw 2.296 3.040 ... (remaining 74384 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.760 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.006 0.070 9666 Z= 0.413 Angle : 0.959 13.638 13128 Z= 0.539 Chirality : 0.055 0.307 1467 Planarity : 0.006 0.065 1661 Dihedral : 15.401 85.516 3355 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.51 % Allowed : 14.69 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -5.53 (0.18), residues: 1203 helix: -4.57 (0.11), residues: 373 sheet: -3.27 (0.28), residues: 247 loop : -3.13 (0.22), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 258 HIS 0.010 0.002 HIS R 250 PHE 0.026 0.002 PHE R 264 TYR 0.054 0.002 TYR B 59 ARG 0.006 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 209 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7451 (ttmt) cc_final: 0.7246 (tmtt) REVERT: A 287 TYR cc_start: 0.7042 (m-10) cc_final: 0.6792 (m-10) REVERT: B 129 ARG cc_start: 0.7525 (ttt-90) cc_final: 0.7194 (mtp180) REVERT: B 291 ASP cc_start: 0.7748 (t0) cc_final: 0.7494 (t0) REVERT: D 13 GLN cc_start: 0.7547 (pp30) cc_final: 0.7347 (pp30) REVERT: D 18 ARG cc_start: 0.7619 (tpp-160) cc_final: 0.7237 (tpp80) REVERT: D 19 LYS cc_start: 0.8430 (tmmt) cc_final: 0.8044 (tttt) REVERT: D 109 ASP cc_start: 0.7976 (t0) cc_final: 0.7754 (t0) REVERT: D 139 VAL cc_start: 0.8383 (t) cc_final: 0.8066 (p) REVERT: D 188 LEU cc_start: 0.8942 (mp) cc_final: 0.8739 (mp) REVERT: E 21 ASP cc_start: 0.8373 (m-30) cc_final: 0.8151 (t0) REVERT: E 24 GLN cc_start: 0.8334 (tp40) cc_final: 0.7791 (tm-30) REVERT: R 39 TYR cc_start: 0.8538 (t80) cc_final: 0.8074 (t80) REVERT: R 231 MET cc_start: 0.7937 (tmm) cc_final: 0.7691 (tmm) outliers start: 5 outliers final: 2 residues processed: 212 average time/residue: 0.2717 time to fit residues: 75.4397 Evaluate side-chains 151 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 295 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 333 GLN B 62 HIS B 142 HIS B 266 HIS B 295 ASN D 77 ASN D 82 GLN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 HIS ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 131 GLN R 250 HIS R 408 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.116127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.087446 restraints weight = 20046.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.089247 restraints weight = 13275.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.090049 restraints weight = 9945.854| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9666 Z= 0.190 Angle : 0.630 8.764 13128 Z= 0.332 Chirality : 0.042 0.162 1467 Planarity : 0.005 0.058 1661 Dihedral : 6.128 35.535 1321 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.14 % Allowed : 17.53 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.40 (0.20), residues: 1203 helix: -3.20 (0.19), residues: 368 sheet: -2.76 (0.29), residues: 251 loop : -2.72 (0.23), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 82 HIS 0.007 0.001 HIS B 266 PHE 0.015 0.001 PHE A 191 TYR 0.018 0.001 TYR R 145 ARG 0.006 0.000 ARG D 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8514 (ttm110) cc_final: 0.8310 (ttm-80) REVERT: A 54 LYS cc_start: 0.7456 (ttmt) cc_final: 0.7131 (tmtt) REVERT: A 287 TYR cc_start: 0.7291 (m-10) cc_final: 0.7048 (m-10) REVERT: A 333 GLN cc_start: 0.8628 (tp40) cc_final: 0.7950 (tm-30) REVERT: B 129 ARG cc_start: 0.7906 (ttt-90) cc_final: 0.7531 (mtp180) REVERT: B 278 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.7092 (m-10) REVERT: B 294 CYS cc_start: 0.8827 (m) cc_final: 0.8378 (m) REVERT: B 295 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.7641 (p0) REVERT: D 14 PRO cc_start: 0.7494 (Cg_endo) cc_final: 0.7231 (Cg_exo) REVERT: D 83 MET cc_start: 0.6524 (ptp) cc_final: 0.6293 (ptp) REVERT: D 188 LEU cc_start: 0.8983 (mp) cc_final: 0.8638 (mp) REVERT: D 235 TYR cc_start: 0.7605 (m-80) cc_final: 0.7375 (m-80) REVERT: E 21 ASP cc_start: 0.8542 (m-30) cc_final: 0.8225 (t0) REVERT: E 24 GLN cc_start: 0.8272 (tp40) cc_final: 0.7601 (tm-30) REVERT: R 39 TYR cc_start: 0.8365 (t80) cc_final: 0.7965 (t80) REVERT: R 131 GLN cc_start: 0.8375 (tt0) cc_final: 0.7541 (tm-30) REVERT: R 140 SER cc_start: 0.8955 (m) cc_final: 0.8704 (p) REVERT: R 231 MET cc_start: 0.7737 (tmm) cc_final: 0.7411 (tmm) outliers start: 31 outliers final: 17 residues processed: 197 average time/residue: 0.2436 time to fit residues: 64.7227 Evaluate side-chains 160 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 339 HIS Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 401 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 48 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 63 optimal weight: 30.0000 chunk 30 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 239 ASN C 44 HIS ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 HIS ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 361 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.110907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.085139 restraints weight = 20908.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.084448 restraints weight = 13181.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.085062 restraints weight = 13192.016| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9666 Z= 0.350 Angle : 0.674 7.582 13128 Z= 0.360 Chirality : 0.045 0.149 1467 Planarity : 0.004 0.059 1661 Dihedral : 6.237 35.500 1321 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 4.66 % Allowed : 20.16 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.87 (0.22), residues: 1203 helix: -2.49 (0.23), residues: 371 sheet: -2.51 (0.30), residues: 250 loop : -2.58 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.022 0.002 PHE R 264 TYR 0.026 0.002 TYR R 145 ARG 0.007 0.001 ARG D 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8916 (pp) REVERT: A 54 LYS cc_start: 0.7405 (ttmt) cc_final: 0.7124 (tmtt) REVERT: A 287 TYR cc_start: 0.7384 (m-10) cc_final: 0.7133 (m-10) REVERT: A 333 GLN cc_start: 0.8566 (tp40) cc_final: 0.7987 (tm-30) REVERT: B 68 ARG cc_start: 0.8409 (tpt90) cc_final: 0.8151 (tpt90) REVERT: B 188 MET cc_start: 0.7999 (mmm) cc_final: 0.7622 (tpt) REVERT: B 198 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8318 (pt) REVERT: B 278 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7055 (m-10) REVERT: B 295 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.7891 (p0) REVERT: D 188 LEU cc_start: 0.8977 (mp) cc_final: 0.8700 (mp) REVERT: D 235 TYR cc_start: 0.7778 (m-80) cc_final: 0.7536 (m-80) REVERT: E 21 ASP cc_start: 0.8551 (m-30) cc_final: 0.8233 (t0) REVERT: E 24 GLN cc_start: 0.8133 (tp40) cc_final: 0.7564 (tm-30) REVERT: R 131 GLN cc_start: 0.8517 (tt0) cc_final: 0.7663 (tm-30) REVERT: R 231 MET cc_start: 0.7796 (tmm) cc_final: 0.7525 (tmm) REVERT: R 401 CYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8701 (m) outliers start: 46 outliers final: 30 residues processed: 185 average time/residue: 0.2221 time to fit residues: 57.8303 Evaluate side-chains 176 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 339 HIS Chi-restraints excluded: chain R residue 351 THR Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 401 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 86 optimal weight: 5.9990 chunk 94 optimal weight: 0.0770 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 69 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 overall best weight: 1.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS C 44 HIS R 361 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.113219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.086535 restraints weight = 20541.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.086975 restraints weight = 13794.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.087651 restraints weight = 12266.010| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9666 Z= 0.226 Angle : 0.605 7.599 13128 Z= 0.319 Chirality : 0.042 0.148 1467 Planarity : 0.004 0.061 1661 Dihedral : 5.902 42.217 1321 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 4.15 % Allowed : 22.59 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.48 (0.22), residues: 1203 helix: -1.98 (0.24), residues: 368 sheet: -2.42 (0.30), residues: 251 loop : -2.42 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 372 PHE 0.017 0.001 PHE B 292 TYR 0.017 0.001 TYR R 145 ARG 0.005 0.000 ARG R 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8566 (ttm-80) cc_final: 0.8296 (ttm110) REVERT: A 36 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8888 (pp) REVERT: A 333 GLN cc_start: 0.8506 (tp40) cc_final: 0.8206 (tm-30) REVERT: B 188 MET cc_start: 0.7832 (mmm) cc_final: 0.7503 (tpt) REVERT: B 278 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7092 (m-10) REVERT: B 292 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7798 (m-80) REVERT: B 294 CYS cc_start: 0.8680 (m) cc_final: 0.8152 (m) REVERT: B 295 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.7862 (p0) REVERT: B 318 LEU cc_start: 0.8043 (mt) cc_final: 0.7837 (mt) REVERT: D 188 LEU cc_start: 0.8966 (mp) cc_final: 0.8717 (mp) REVERT: D 235 TYR cc_start: 0.7724 (m-80) cc_final: 0.7517 (m-80) REVERT: E 21 ASP cc_start: 0.8471 (m-30) cc_final: 0.8232 (t0) REVERT: E 24 GLN cc_start: 0.8101 (tp40) cc_final: 0.7614 (tm-30) REVERT: R 111 ARG cc_start: 0.8253 (tpt170) cc_final: 0.7509 (mpp80) REVERT: R 131 GLN cc_start: 0.8418 (tt0) cc_final: 0.7604 (tm-30) REVERT: R 140 SER cc_start: 0.8833 (m) cc_final: 0.8604 (p) REVERT: R 231 MET cc_start: 0.7695 (tmm) cc_final: 0.7476 (tmm) REVERT: R 382 LEU cc_start: 0.9201 (mt) cc_final: 0.8887 (mt) outliers start: 41 outliers final: 26 residues processed: 182 average time/residue: 0.2331 time to fit residues: 59.8912 Evaluate side-chains 175 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain R residue 137 MET Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 339 HIS Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 401 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 85 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 93 optimal weight: 0.4980 chunk 16 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 295 ASN ** R 361 HIS ** 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 = 0.3715 r_free = 0.3715 target = 0.113587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.086631 restraints weight = 20456.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.086475 restraints weight = 13675.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.087156 restraints weight = 13023.745| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9666 Z= 0.209 Angle : 0.599 7.565 13128 Z= 0.312 Chirality : 0.042 0.147 1467 Planarity : 0.004 0.059 1661 Dihedral : 5.726 42.219 1321 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.66 % Allowed : 23.20 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.23 (0.23), residues: 1203 helix: -1.66 (0.25), residues: 368 sheet: -2.27 (0.31), residues: 244 loop : -2.36 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 339 HIS 0.008 0.001 HIS B 142 PHE 0.022 0.001 PHE E 22 TYR 0.017 0.001 TYR R 145 ARG 0.004 0.000 ARG R 308 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8571 (ttm-80) cc_final: 0.8307 (ttm110) REVERT: A 36 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8864 (pp) REVERT: A 333 GLN cc_start: 0.8487 (tp40) cc_final: 0.8231 (tm-30) REVERT: B 188 MET cc_start: 0.7769 (mmm) cc_final: 0.7562 (tpt) REVERT: B 198 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8404 (pt) REVERT: B 278 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.6963 (m-10) REVERT: B 286 LEU cc_start: 0.8827 (mm) cc_final: 0.8581 (mp) REVERT: B 292 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7837 (m-80) REVERT: B 294 CYS cc_start: 0.8707 (m) cc_final: 0.8195 (m) REVERT: B 295 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7800 (p0) REVERT: B 318 LEU cc_start: 0.8073 (mt) cc_final: 0.7824 (mt) REVERT: D 188 LEU cc_start: 0.8978 (mp) cc_final: 0.8636 (mp) REVERT: D 235 TYR cc_start: 0.7727 (m-80) cc_final: 0.7500 (m-80) REVERT: E 21 ASP cc_start: 0.8458 (m-30) cc_final: 0.8203 (t0) REVERT: E 24 GLN cc_start: 0.8073 (tp40) cc_final: 0.7597 (tm-30) REVERT: R 29 MET cc_start: 0.8376 (ppp) cc_final: 0.8070 (ppp) REVERT: R 34 GLU cc_start: 0.8086 (pp20) cc_final: 0.7593 (pp20) REVERT: R 111 ARG cc_start: 0.8229 (tpt170) cc_final: 0.7492 (mpp80) REVERT: R 131 GLN cc_start: 0.8446 (tt0) cc_final: 0.7524 (tm-30) REVERT: R 140 SER cc_start: 0.8868 (m) cc_final: 0.8621 (p) REVERT: R 231 MET cc_start: 0.7661 (tmm) cc_final: 0.7434 (tmm) outliers start: 46 outliers final: 34 residues processed: 186 average time/residue: 0.2068 time to fit residues: 54.6663 Evaluate side-chains 179 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 137 MET Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 339 HIS Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 401 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 117 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 113 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.112620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.085724 restraints weight = 20514.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.085663 restraints weight = 13396.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.086447 restraints weight = 12323.646| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9666 Z= 0.251 Angle : 0.621 7.228 13128 Z= 0.323 Chirality : 0.043 0.160 1467 Planarity : 0.004 0.059 1661 Dihedral : 5.743 44.868 1321 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 5.27 % Allowed : 24.11 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.08 (0.23), residues: 1203 helix: -1.52 (0.25), residues: 368 sheet: -2.21 (0.32), residues: 243 loop : -2.27 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 111 HIS 0.004 0.001 HIS A 213 PHE 0.018 0.002 PHE R 365 TYR 0.018 0.002 TYR R 145 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 142 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8576 (ttm-80) cc_final: 0.8323 (ttm110) REVERT: A 36 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8880 (pp) REVERT: A 333 GLN cc_start: 0.8500 (tp40) cc_final: 0.8246 (tm-30) REVERT: B 198 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8382 (pt) REVERT: B 278 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.6898 (m-10) REVERT: B 286 LEU cc_start: 0.8861 (mm) cc_final: 0.8627 (mp) REVERT: B 292 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7951 (m-80) REVERT: B 294 CYS cc_start: 0.8728 (m) cc_final: 0.8238 (m) REVERT: B 295 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.7834 (p0) REVERT: B 318 LEU cc_start: 0.8103 (mt) cc_final: 0.7821 (mt) REVERT: E 21 ASP cc_start: 0.8481 (m-30) cc_final: 0.8195 (t0) REVERT: E 24 GLN cc_start: 0.8059 (tp40) cc_final: 0.7542 (tm-30) REVERT: R 34 GLU cc_start: 0.8149 (pp20) cc_final: 0.7666 (pp20) REVERT: R 111 ARG cc_start: 0.8218 (tpt170) cc_final: 0.7488 (mpp80) REVERT: R 131 GLN cc_start: 0.8462 (tt0) cc_final: 0.7514 (tm-30) REVERT: R 140 SER cc_start: 0.8868 (m) cc_final: 0.8632 (p) REVERT: R 231 MET cc_start: 0.7708 (tmm) cc_final: 0.7483 (tmm) REVERT: R 401 CYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8678 (m) outliers start: 52 outliers final: 34 residues processed: 183 average time/residue: 0.2110 time to fit residues: 54.8880 Evaluate side-chains 174 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 137 MET Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 295 TRP Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 339 HIS Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 401 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 30 optimal weight: 0.3980 chunk 110 optimal weight: 0.1980 chunk 83 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 117 optimal weight: 0.3980 chunk 118 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.117107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.090598 restraints weight = 20296.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.090099 restraints weight = 13056.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.090758 restraints weight = 11440.893| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9666 Z= 0.160 Angle : 0.591 8.116 13128 Z= 0.305 Chirality : 0.041 0.156 1467 Planarity : 0.003 0.059 1661 Dihedral : 5.374 48.870 1321 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.55 % Allowed : 26.44 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -2.74 (0.23), residues: 1203 helix: -1.13 (0.26), residues: 368 sheet: -2.09 (0.31), residues: 259 loop : -2.09 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 111 HIS 0.010 0.001 HIS B 142 PHE 0.024 0.001 PHE E 22 TYR 0.016 0.001 TYR R 39 ARG 0.003 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8777 (pp) REVERT: B 188 MET cc_start: 0.7850 (tpt) cc_final: 0.7601 (mmm) REVERT: B 278 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.6825 (m-10) REVERT: B 294 CYS cc_start: 0.8607 (m) cc_final: 0.8283 (m) REVERT: B 295 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7636 (p0) REVERT: D 235 TYR cc_start: 0.7701 (m-80) cc_final: 0.7459 (m-80) REVERT: E 21 ASP cc_start: 0.8488 (m-30) cc_final: 0.8193 (t0) REVERT: E 24 GLN cc_start: 0.7991 (tp40) cc_final: 0.7535 (tm-30) REVERT: R 34 GLU cc_start: 0.8041 (pp20) cc_final: 0.7583 (pp20) REVERT: R 140 SER cc_start: 0.8784 (m) cc_final: 0.8560 (p) outliers start: 35 outliers final: 26 residues processed: 179 average time/residue: 0.2066 time to fit residues: 52.5178 Evaluate side-chains 160 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 45 HIS Chi-restraints excluded: chain R residue 137 MET Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 339 HIS Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 401 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 15 optimal weight: 0.0270 chunk 41 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 73 optimal weight: 0.0050 overall best weight: 0.5854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS R 361 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.117825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.090646 restraints weight = 20582.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.091520 restraints weight = 13440.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.092326 restraints weight = 10493.756| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9666 Z= 0.161 Angle : 0.595 11.043 13128 Z= 0.305 Chirality : 0.041 0.143 1467 Planarity : 0.003 0.057 1661 Dihedral : 5.157 45.962 1321 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.65 % Allowed : 26.75 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -2.43 (0.24), residues: 1203 helix: -0.80 (0.27), residues: 372 sheet: -1.89 (0.31), residues: 259 loop : -1.96 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 339 HIS 0.004 0.001 HIS R 372 PHE 0.012 0.001 PHE R 309 TYR 0.016 0.001 TYR R 39 ARG 0.005 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8733 (pp) REVERT: B 68 ARG cc_start: 0.7738 (tpt90) cc_final: 0.7494 (mmm160) REVERT: B 198 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8386 (pt) REVERT: B 294 CYS cc_start: 0.8632 (m) cc_final: 0.8313 (m) REVERT: B 295 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7644 (p0) REVERT: D 235 TYR cc_start: 0.7756 (m-80) cc_final: 0.7533 (m-80) REVERT: E 21 ASP cc_start: 0.8475 (m-30) cc_final: 0.8225 (t0) REVERT: E 24 GLN cc_start: 0.7951 (tp40) cc_final: 0.7540 (tm-30) REVERT: R 34 GLU cc_start: 0.7962 (pp20) cc_final: 0.7504 (pp20) REVERT: R 312 PHE cc_start: 0.7952 (t80) cc_final: 0.7670 (t80) outliers start: 36 outliers final: 27 residues processed: 176 average time/residue: 0.2060 time to fit residues: 51.7232 Evaluate side-chains 166 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 45 HIS Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 339 HIS Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 401 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 97 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 94 optimal weight: 0.0670 chunk 22 optimal weight: 30.0000 chunk 14 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS R 339 HIS R 361 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.113764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.087538 restraints weight = 20615.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.088751 restraints weight = 14865.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.089571 restraints weight = 12730.159| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9666 Z= 0.263 Angle : 0.642 9.354 13128 Z= 0.332 Chirality : 0.043 0.141 1467 Planarity : 0.004 0.055 1661 Dihedral : 5.352 44.724 1321 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.05 % Allowed : 26.75 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.41 (0.24), residues: 1203 helix: -0.80 (0.26), residues: 377 sheet: -1.87 (0.32), residues: 249 loop : -1.96 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 339 HIS 0.004 0.001 HIS A 213 PHE 0.026 0.002 PHE E 22 TYR 0.021 0.002 TYR R 39 ARG 0.009 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8136 (mtm-85) cc_final: 0.7887 (ptp90) REVERT: A 36 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8907 (pp) REVERT: A 208 ARG cc_start: 0.7972 (ttm110) cc_final: 0.7616 (mtt90) REVERT: B 198 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8467 (pt) REVERT: B 294 CYS cc_start: 0.8631 (m) cc_final: 0.8284 (m) REVERT: B 295 ASN cc_start: 0.8332 (OUTLIER) cc_final: 0.7854 (p0) REVERT: D 235 TYR cc_start: 0.7767 (m-80) cc_final: 0.7521 (m-80) REVERT: E 21 ASP cc_start: 0.8364 (m-30) cc_final: 0.8086 (t0) REVERT: E 24 GLN cc_start: 0.7839 (tp40) cc_final: 0.7635 (tm-30) REVERT: R 34 GLU cc_start: 0.7879 (pp20) cc_final: 0.7387 (pp20) REVERT: R 131 GLN cc_start: 0.8327 (tt0) cc_final: 0.7503 (tm-30) REVERT: R 144 MET cc_start: 0.7985 (tmm) cc_final: 0.7784 (tmm) REVERT: R 401 CYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8572 (m) outliers start: 40 outliers final: 30 residues processed: 166 average time/residue: 0.1964 time to fit residues: 46.3923 Evaluate side-chains 164 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 45 HIS Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 339 HIS Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 401 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 110 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS R 361 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.113274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.086741 restraints weight = 20850.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.088048 restraints weight = 14851.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.088868 restraints weight = 12320.358| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9666 Z= 0.266 Angle : 0.656 11.731 13128 Z= 0.335 Chirality : 0.043 0.143 1467 Planarity : 0.004 0.055 1661 Dihedral : 5.427 45.359 1321 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 4.15 % Allowed : 26.55 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.40 (0.24), residues: 1203 helix: -0.79 (0.26), residues: 377 sheet: -1.86 (0.32), residues: 249 loop : -1.96 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.011 0.001 HIS R 339 PHE 0.018 0.001 PHE D 68 TYR 0.022 0.002 TYR R 39 ARG 0.008 0.000 ARG A 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8121 (mtm-85) cc_final: 0.7876 (ptp90) REVERT: A 36 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8907 (pp) REVERT: A 208 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7610 (mtt90) REVERT: B 198 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8473 (pt) REVERT: B 294 CYS cc_start: 0.8677 (m) cc_final: 0.8239 (m) REVERT: B 295 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.7876 (p0) REVERT: D 235 TYR cc_start: 0.7734 (m-80) cc_final: 0.7512 (m-80) REVERT: E 21 ASP cc_start: 0.8389 (m-30) cc_final: 0.8058 (t0) REVERT: E 24 GLN cc_start: 0.7866 (tp40) cc_final: 0.7640 (tm-30) REVERT: R 34 GLU cc_start: 0.7924 (pp20) cc_final: 0.7411 (pp20) REVERT: R 131 GLN cc_start: 0.8312 (tt0) cc_final: 0.7486 (tm-30) REVERT: R 401 CYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8582 (m) outliers start: 41 outliers final: 34 residues processed: 162 average time/residue: 0.2035 time to fit residues: 47.2443 Evaluate side-chains 168 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 45 HIS Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 313 LEU Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 401 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 73 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 67 optimal weight: 0.0970 chunk 25 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.115316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.087654 restraints weight = 20301.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.089044 restraints weight = 12766.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.089682 restraints weight = 10496.869| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9666 Z= 0.194 Angle : 0.648 12.906 13128 Z= 0.327 Chirality : 0.043 0.147 1467 Planarity : 0.003 0.059 1661 Dihedral : 5.317 46.892 1321 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.15 % Allowed : 26.65 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -2.22 (0.24), residues: 1203 helix: -0.52 (0.27), residues: 374 sheet: -1.79 (0.32), residues: 249 loop : -1.93 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.003 0.001 HIS B 142 PHE 0.025 0.001 PHE E 22 TYR 0.022 0.001 TYR R 39 ARG 0.007 0.000 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3293.35 seconds wall clock time: 59 minutes 47.56 seconds (3587.56 seconds total)