Starting phenix.real_space_refine on Fri Mar 6 02:08:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d45_30570/03_2026/7d45_30570.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d45_30570/03_2026/7d45_30570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d45_30570/03_2026/7d45_30570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d45_30570/03_2026/7d45_30570.map" model { file = "/net/cci-nas-00/data/ceres_data/7d45_30570/03_2026/7d45_30570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d45_30570/03_2026/7d45_30570.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 142 5.16 5 C 17407 2.51 5 N 4827 2.21 5 O 5152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 142 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27529 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2265 Classifications: {'peptide': 293} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2256 Classifications: {'peptide': 291} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2476 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "D" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2515 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2445 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 11, 'TRANS': 334} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 323 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 99 Chain: "F" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2465 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 12, 'TRANS': 337} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 99 Chain: "G" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "H" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "I" Number of atoms: 3355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3355 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 3363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3363 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 409} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 889 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 4, 'TRANS': 171} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 585 Unresolved non-hydrogen angles: 743 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'ARG:plan': 14, 'PHE:plan': 6, 'TYR:plan': 9, 'GLN:plan1': 3, 'HIS:plan': 3, 'GLU:plan': 18, 'ASP:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 340 Time building chain proxies: 5.84, per 1000 atoms: 0.21 Number of scatterers: 27529 At special positions: 0 Unit cell: (164.64, 167.58, 163.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 142 16.00 P 1 15.00 O 5152 8.00 N 4827 7.00 C 17407 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6938 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 39 sheets defined 40.1% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 42 through 58 removed outlier: 3.646A pdb=" N ALA A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'A' and resid 62 through 76 removed outlier: 3.664A pdb=" N SER A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 4.670A pdb=" N ARG A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.564A pdb=" N LYS A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 removed outlier: 4.006A pdb=" N GLY A 184 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 removed outlier: 4.024A pdb=" N ALA A 190 " --> pdb=" O MET A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.572A pdb=" N MET A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 4.066A pdb=" N TYR A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 305 removed outlier: 4.345A pdb=" N ASP A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 17 removed outlier: 3.966A pdb=" N ASP B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 36 Processing helix chain 'B' and resid 45 through 60 removed outlier: 3.728A pdb=" N SER B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 77 removed outlier: 3.621A pdb=" N SER B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 116 removed outlier: 3.804A pdb=" N LYS B 90 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASN B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 144 Processing helix chain 'B' and resid 160 through 170 removed outlier: 3.515A pdb=" N MET B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.602A pdb=" N MET B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 222 " --> pdb=" O CYS B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 removed outlier: 3.750A pdb=" N VAL B 246 " --> pdb=" O GLN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.641A pdb=" N GLU C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 49 removed outlier: 3.579A pdb=" N MET C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.510A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 96 Processing helix chain 'C' and resid 128 through 146 removed outlier: 3.947A pdb=" N ASN C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 159 removed outlier: 4.076A pdb=" N LEU C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLU C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N HIS C 158 " --> pdb=" O GLN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 181 removed outlier: 3.668A pdb=" N ALA C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 209 removed outlier: 4.149A pdb=" N GLU C 202 " --> pdb=" O CYS C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 251 through 262 removed outlier: 3.885A pdb=" N HIS C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 304 removed outlier: 3.530A pdb=" N LEU C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.725A pdb=" N LEU C 339 " --> pdb=" O TYR C 335 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C 341 " --> pdb=" O TYR C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 removed outlier: 3.809A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL C 350 " --> pdb=" O ASP C 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 346 through 350' Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 30 through 46 Processing helix chain 'D' and resid 54 through 72 removed outlier: 4.076A pdb=" N ARG D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 97 removed outlier: 3.581A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 146 Processing helix chain 'D' and resid 146 through 156 removed outlier: 3.809A pdb=" N ASN D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 220 through 222 No H-bonds generated for 'chain 'D' and resid 220 through 222' Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.596A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 344 removed outlier: 3.854A pdb=" N ILE D 336 " --> pdb=" O ALA D 332 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR D 337 " --> pdb=" O PRO D 333 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ARG D 338 " --> pdb=" O SER D 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 85 through 94 Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 114 through 124 Processing helix chain 'E' and resid 183 through 190 removed outlier: 3.645A pdb=" N LEU E 187 " --> pdb=" O LYS E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 218 Processing helix chain 'E' and resid 223 through 228 Processing helix chain 'E' and resid 228 through 235 Processing helix chain 'E' and resid 236 through 238 No H-bonds generated for 'chain 'E' and resid 236 through 238' Processing helix chain 'E' and resid 279 through 293 removed outlier: 4.189A pdb=" N ASN E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TRP E 290 " --> pdb=" O ARG E 286 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU E 293 " --> pdb=" O ARG E 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 46 removed outlier: 3.738A pdb=" N VAL F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 67 Processing helix chain 'F' and resid 85 through 94 Processing helix chain 'F' and resid 95 through 97 No H-bonds generated for 'chain 'F' and resid 95 through 97' Processing helix chain 'F' and resid 113 through 125 removed outlier: 4.203A pdb=" N VAL F 117 " --> pdb=" O ALA F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 190 Processing helix chain 'F' and resid 208 through 218 removed outlier: 3.707A pdb=" N VAL F 212 " --> pdb=" O LYS F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 228 Processing helix chain 'F' and resid 228 through 236 Processing helix chain 'F' and resid 277 through 292 removed outlier: 3.747A pdb=" N CYS F 281 " --> pdb=" O PRO F 277 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TRP F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 181 removed outlier: 3.827A pdb=" N SER G 181 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 Processing helix chain 'G' and resid 204 through 216 Processing helix chain 'G' and resid 221 through 239 Processing helix chain 'G' and resid 247 through 267 removed outlier: 4.414A pdb=" N VAL G 253 " --> pdb=" O SER G 249 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 270 through 286 Processing helix chain 'G' and resid 292 through 312 removed outlier: 3.787A pdb=" N ILE G 312 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 325 removed outlier: 3.698A pdb=" N GLN G 317 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN G 325 " --> pdb=" O ARG G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 351 Processing helix chain 'G' and resid 369 through 378 Processing helix chain 'G' and resid 390 through 395 removed outlier: 3.701A pdb=" N VAL G 394 " --> pdb=" O ALA G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 419 through 431 Processing helix chain 'G' and resid 459 through 463 Processing helix chain 'G' and resid 512 through 517 Processing helix chain 'H' and resid 177 through 181 Processing helix chain 'H' and resid 191 through 196 removed outlier: 3.646A pdb=" N GLN H 194 " --> pdb=" O SER H 191 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET H 196 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 216 Processing helix chain 'H' and resid 221 through 239 Processing helix chain 'H' and resid 247 through 267 removed outlier: 4.638A pdb=" N VAL H 253 " --> pdb=" O SER H 249 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 270 through 285 Processing helix chain 'H' and resid 292 through 312 Processing helix chain 'H' and resid 313 through 324 Processing helix chain 'H' and resid 340 through 352 Processing helix chain 'H' and resid 368 through 378 removed outlier: 4.394A pdb=" N THR H 372 " --> pdb=" O GLU H 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 390 through 395 removed outlier: 3.622A pdb=" N VAL H 394 " --> pdb=" O ALA H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 419 through 430 Processing helix chain 'H' and resid 459 through 463 Processing helix chain 'H' and resid 508 through 512 removed outlier: 3.853A pdb=" N VAL H 512 " --> pdb=" O CYS H 509 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 68 removed outlier: 3.763A pdb=" N LEU I 68 " --> pdb=" O ARG I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 86 removed outlier: 3.514A pdb=" N THR I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 108 removed outlier: 3.954A pdb=" N LYS I 108 " --> pdb=" O GLU I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 142 Processing helix chain 'I' and resid 161 through 176 Processing helix chain 'I' and resid 196 through 199 Processing helix chain 'I' and resid 227 through 232 removed outlier: 3.996A pdb=" N GLN I 232 " --> pdb=" O SER I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 263 removed outlier: 3.761A pdb=" N THR I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN I 263 " --> pdb=" O LEU I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 279 Processing helix chain 'I' and resid 302 through 315 removed outlier: 3.637A pdb=" N ARG I 315 " --> pdb=" O ALA I 311 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 342 removed outlier: 3.758A pdb=" N ILE I 342 " --> pdb=" O ARG I 339 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 74 through 86 Processing helix chain 'J' and resid 98 through 108 removed outlier: 3.635A pdb=" N LYS J 108 " --> pdb=" O GLU J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 142 Processing helix chain 'J' and resid 161 through 176 removed outlier: 3.712A pdb=" N GLU J 175 " --> pdb=" O ARG J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 235 Processing helix chain 'J' and resid 253 through 263 removed outlier: 3.636A pdb=" N ALA J 257 " --> pdb=" O SER J 253 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN J 263 " --> pdb=" O LEU J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 277 Processing helix chain 'J' and resid 302 through 314 Processing helix chain 'J' and resid 338 through 342 Processing helix chain 'K' and resid 52 through 56 removed outlier: 3.852A pdb=" N ILE K 55 " --> pdb=" O ARG K 52 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG K 56 " --> pdb=" O ARG K 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 52 through 56' Processing helix chain 'K' and resid 60 through 65 removed outlier: 3.937A pdb=" N GLY K 65 " --> pdb=" O LEU K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 118 Processing helix chain 'K' and resid 122 through 139 Processing helix chain 'K' and resid 146 through 154 Processing helix chain 'K' and resid 169 through 180 removed outlier: 3.519A pdb=" N GLU K 173 " --> pdb=" O GLU K 169 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 177 removed outlier: 6.016A pdb=" N THR A 124 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE A 194 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LEU A 126 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLY A 196 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL A 193 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL A 229 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL A 195 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE A 226 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N PHE A 285 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A 228 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA3, first strand: chain 'B' and resid 124 through 127 removed outlier: 6.908A pdb=" N ILE B 125 " --> pdb=" O TYR B 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 193 through 194 removed outlier: 5.799A pdb=" N VAL B 193 " --> pdb=" O TYR B 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 207 through 209 Processing sheet with id=AA6, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AA7, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.517A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL C 164 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ILE C 233 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N MET C 166 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL C 189 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N MET C 217 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL C 191 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR C 214 " --> pdb=" O ARG G 483 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N LEU G 485 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL C 216 " --> pdb=" O LEU G 485 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 238 through 239 removed outlier: 3.718A pdb=" N THR C 238 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 214 through 218 removed outlier: 3.996A pdb=" N ALA D 192 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE D 168 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU D 323 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AB2, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AB3, first strand: chain 'E' and resid 102 through 103 removed outlier: 3.509A pdb=" N TYR E 205 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA E 202 " --> pdb=" O ARG E 133 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ARG E 133 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU E 204 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU E 131 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE E 266 " --> pdb=" O MET E 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 167 through 171 removed outlier: 6.374A pdb=" N GLY E 159 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET E 170 " --> pdb=" O PHE E 157 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE E 157 " --> pdb=" O MET E 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 362 through 364 removed outlier: 6.415A pdb=" N GLN E 363 " --> pdb=" O ILE E 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 374 through 375 removed outlier: 5.701A pdb=" N LEU E 391 " --> pdb=" O ILE E 409 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 76 through 79 removed outlier: 6.117A pdb=" N VAL F 53 " --> pdb=" O ILE F 78 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ALA F 5 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL F 54 " --> pdb=" O ALA F 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL F 7 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL F 6 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER F 105 " --> pdb=" O HIS F 203 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N HIS F 203 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ALA F 202 " --> pdb=" O ARG F 133 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N ARG F 133 " --> pdb=" O ALA F 202 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LEU F 204 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F 131 " --> pdb=" O LEU F 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 167 through 171 removed outlier: 3.637A pdb=" N ALA F 171 " --> pdb=" O PHE F 157 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE F 157 " --> pdb=" O ALA F 171 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL I 238 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL I 202 " --> pdb=" O PHE I 215 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE I 215 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA I 204 " --> pdb=" O LEU I 213 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG I 211 " --> pdb=" O ASP I 206 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE I 287 " --> pdb=" O VAL I 212 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N MET I 181 " --> pdb=" O HIS I 288 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N HIS I 290 " --> pdb=" O MET I 181 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N MET I 183 " --> pdb=" O HIS I 290 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR I 292 " --> pdb=" O MET I 183 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N PHE I 185 " --> pdb=" O THR I 292 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR I 182 " --> pdb=" O ILE I 251 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER I 250 " --> pdb=" O LEU I 150 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 119 through 120 removed outlier: 3.755A pdb=" N THR I 91 " --> pdb=" O VAL I 119 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER I 250 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR I 182 " --> pdb=" O ILE I 251 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 182 through 183 Processing sheet with id=AC2, first strand: chain 'F' and resid 352 through 354 removed outlier: 7.057A pdb=" N VAL F 352 " --> pdb=" O ILE F 370 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 374 through 375 removed outlier: 6.132A pdb=" N VAL F 374 " --> pdb=" O LEU F 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 332 through 334 removed outlier: 7.244A pdb=" N ILE G 333 " --> pdb=" O VAL G 359 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL G 361 " --> pdb=" O ILE G 333 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 414 through 416 Processing sheet with id=AC6, first strand: chain 'G' and resid 436 through 437 removed outlier: 7.470A pdb=" N VAL G 436 " --> pdb=" O ILE G 501 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 466 through 467 removed outlier: 3.619A pdb=" N ARG G 467 " --> pdb=" O HIS G 470 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 386 through 387 removed outlier: 6.979A pdb=" N ILE H 333 " --> pdb=" O VAL H 359 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL H 361 " --> pdb=" O ILE H 333 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL H 335 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL H 332 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS H 400 " --> pdb=" O VAL H 332 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 407 through 408 Processing sheet with id=AD1, first strand: chain 'H' and resid 436 through 437 removed outlier: 7.108A pdb=" N VAL H 436 " --> pdb=" O ILE H 501 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 155 through 157 Processing sheet with id=AD3, first strand: chain 'I' and resid 355 through 356 removed outlier: 3.697A pdb=" N ILE I 374 " --> pdb=" O ILE I 355 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 423 through 424 Processing sheet with id=AD5, first strand: chain 'J' and resid 94 through 95 Processing sheet with id=AD6, first strand: chain 'J' and resid 155 through 157 Processing sheet with id=AD7, first strand: chain 'J' and resid 186 through 187 Processing sheet with id=AD8, first strand: chain 'J' and resid 212 through 217 removed outlier: 6.322A pdb=" N ALA J 204 " --> pdb=" O LEU J 213 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE J 215 " --> pdb=" O VAL J 202 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL J 202 " --> pdb=" O PHE J 215 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 355 through 356 removed outlier: 6.421A pdb=" N ILE J 355 " --> pdb=" O ILE J 374 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE J 373 " --> pdb=" O LEU J 391 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL J 390 " --> pdb=" O ILE J 408 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'J' and resid 367 through 368 removed outlier: 6.118A pdb=" N VAL J 367 " --> pdb=" O ILE J 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 423 through 424 removed outlier: 3.555A pdb=" N THR J 424 " --> pdb=" O ILE J 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'K' and resid 41 through 46 removed outlier: 6.911A pdb=" N TYR K 32 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASP K 83 " --> pdb=" O ILE K 73 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL K 75 " --> pdb=" O TYR K 81 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TYR K 81 " --> pdb=" O VAL K 75 " (cutoff:3.500A) 1066 hydrogen bonds defined for protein. 3003 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.50 Time building geometry restraints manager: 2.94 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: 9217 1.34 - 1.46: 4840 1.46 - 1.58: 13726 1.58 - 1.70: 4 1.70 - 1.82: 216 Bond restraints: 28003 Sorted by residual: bond pdb=" CA ALA G 349 " pdb=" C ALA G 349 " ideal model delta sigma weight residual 1.522 1.467 0.055 1.31e-02 5.83e+03 1.74e+01 bond pdb=" CA LEU C 96 " pdb=" C LEU C 96 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.48e-02 4.57e+03 1.03e+01 bond pdb=" CA ARG J 121 " pdb=" CB ARG J 121 " ideal model delta sigma weight residual 1.524 1.483 0.041 1.33e-02 5.65e+03 9.40e+00 bond pdb=" CA ALA D 258 " pdb=" C ALA D 258 " ideal model delta sigma weight residual 1.523 1.485 0.039 1.34e-02 5.57e+03 8.30e+00 bond pdb=" C SER C 275 " pdb=" N PRO C 276 " ideal model delta sigma weight residual 1.331 1.309 0.022 7.90e-03 1.60e+04 7.97e+00 ... (remaining 27998 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 37725 3.64 - 7.27: 281 7.27 - 10.91: 18 10.91 - 14.55: 0 14.55 - 18.18: 1 Bond angle restraints: 38025 Sorted by residual: angle pdb=" C THR G 241 " pdb=" N THR G 242 " pdb=" CA THR G 242 " ideal model delta sigma weight residual 122.67 104.49 18.18 2.19e+00 2.09e-01 6.89e+01 angle pdb=" N VAL J 178 " pdb=" CA VAL J 178 " pdb=" C VAL J 178 " ideal model delta sigma weight residual 113.53 106.31 7.22 9.80e-01 1.04e+00 5.42e+01 angle pdb=" N PRO F 24 " pdb=" CA PRO F 24 " pdb=" CB PRO F 24 " ideal model delta sigma weight residual 103.25 110.96 -7.71 1.05e+00 9.07e-01 5.39e+01 angle pdb=" N PRO F 26 " pdb=" CA PRO F 26 " pdb=" CB PRO F 26 " ideal model delta sigma weight residual 103.25 110.15 -6.90 1.05e+00 9.07e-01 4.32e+01 angle pdb=" N PRO J 40 " pdb=" CA PRO J 40 " pdb=" CB PRO J 40 " ideal model delta sigma weight residual 103.00 110.21 -7.21 1.10e+00 8.26e-01 4.29e+01 ... (remaining 38020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 14980 17.69 - 35.39: 1650 35.39 - 53.08: 318 53.08 - 70.77: 37 70.77 - 88.47: 19 Dihedral angle restraints: 17004 sinusoidal: 6339 harmonic: 10665 Sorted by residual: dihedral pdb=" CA ALA B 197 " pdb=" C ALA B 197 " pdb=" N GLU B 198 " pdb=" CA GLU B 198 " ideal model delta harmonic sigma weight residual -180.00 -144.57 -35.43 0 5.00e+00 4.00e-02 5.02e+01 dihedral pdb=" CA LYS B 209 " pdb=" C LYS B 209 " pdb=" N ILE B 210 " pdb=" CA ILE B 210 " ideal model delta harmonic sigma weight residual -180.00 -151.37 -28.63 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA HIS D 125 " pdb=" C HIS D 125 " pdb=" N TYR D 126 " pdb=" CA TYR D 126 " ideal model delta harmonic sigma weight residual -180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 17001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3240 0.054 - 0.109: 1063 0.109 - 0.163: 185 0.163 - 0.217: 6 0.217 - 0.271: 3 Chirality restraints: 4497 Sorted by residual: chirality pdb=" CA PRO F 24 " pdb=" N PRO F 24 " pdb=" C PRO F 24 " pdb=" CB PRO F 24 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA PRO J 40 " pdb=" N PRO J 40 " pdb=" C PRO J 40 " pdb=" CB PRO J 40 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA PRO F 26 " pdb=" N PRO F 26 " pdb=" C PRO F 26 " pdb=" CB PRO F 26 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 4494 not shown) Planarity restraints: 4909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 395 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO G 396 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO G 396 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 396 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 395 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.12e+00 pdb=" N PRO H 396 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO H 396 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 396 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 364 " 0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO H 365 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO H 365 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 365 " 0.024 5.00e-02 4.00e+02 ... (remaining 4906 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 619 2.65 - 3.21: 28188 3.21 - 3.77: 41979 3.77 - 4.34: 56774 4.34 - 4.90: 93990 Nonbonded interactions: 221550 Sorted by model distance: nonbonded pdb=" OG1 THR D 76 " pdb=" OG1 THR D 238 " model vdw 2.082 3.040 nonbonded pdb=" O PRO E 95 " pdb=" NZ LYS E 98 " model vdw 2.084 3.120 nonbonded pdb=" OH TYR F 94 " pdb=" OD1 ASP F 213 " model vdw 2.089 3.040 nonbonded pdb=" OD2 ASP J 62 " pdb=" OG SER J 433 " model vdw 2.096 3.040 nonbonded pdb=" O LYS E 235 " pdb=" OG SER E 238 " model vdw 2.124 3.040 ... (remaining 221545 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 253 or resid 268 through 305)) selection = (chain 'B' and (resid 1 through 90 or (resid 91 and (name N or name CA or name C \ or name O or name CB )) or resid 92 through 305)) } ncs_group { reference = (chain 'C' and (resid 8 through 343 or (resid 344 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 345 through 351)) selection = (chain 'D' and (resid 8 through 98 or resid 126 through 351)) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 1 through 11 or resid 25 through 444)) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 41 through 170 or (resid 171 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ )) or resid \ 172 through 467)) selection = (chain 'J' and resid 41 through 467) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 22.980 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 0.009 0.064 28003 Z= 0.379 Angle : 0.919 18.183 38025 Z= 0.525 Chirality : 0.052 0.271 4497 Planarity : 0.005 0.063 4909 Dihedral : 15.228 88.467 10066 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 16.65 % Favored : 83.13 % Rotamer: Outliers : 0.35 % Allowed : 11.64 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.81 (0.12), residues: 3610 helix: -1.98 (0.12), residues: 1258 sheet: -4.19 (0.19), residues: 442 loop : -3.92 (0.12), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 417 TYR 0.030 0.003 TYR J 343 PHE 0.030 0.003 PHE D 177 TRP 0.012 0.002 TRP D 51 HIS 0.011 0.001 HIS G 479 Details of bonding type rmsd covalent geometry : bond 0.00867 (28003) covalent geometry : angle 0.91859 (38025) hydrogen bonds : bond 0.14151 ( 1056) hydrogen bonds : angle 6.97002 ( 3003) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 426 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8212 (tpp) cc_final: 0.7637 (tpt) REVERT: A 210 ILE cc_start: 0.7998 (pt) cc_final: 0.7666 (pt) REVERT: B 187 MET cc_start: 0.8917 (tpp) cc_final: 0.8654 (tpt) REVERT: B 244 GLN cc_start: 0.8504 (tp40) cc_final: 0.8285 (tp-100) REVERT: D 139 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7483 (tm-30) REVERT: D 163 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6332 (mt-10) REVERT: D 184 LYS cc_start: 0.8406 (mmmt) cc_final: 0.7646 (tptt) REVERT: D 203 MET cc_start: 0.8325 (ttt) cc_final: 0.8032 (ttt) REVERT: E 84 MET cc_start: 0.6048 (ttt) cc_final: 0.5842 (ttt) REVERT: E 92 TYR cc_start: 0.7804 (t80) cc_final: 0.7551 (t80) REVERT: E 289 ARG cc_start: 0.6929 (tmt170) cc_final: 0.6212 (tpt170) REVERT: F 125 ASP cc_start: 0.7692 (t0) cc_final: 0.7443 (t0) REVERT: G 195 PHE cc_start: 0.6841 (m-80) cc_final: 0.6156 (m-80) REVERT: G 386 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8109 (pp) REVERT: H 207 MET cc_start: 0.8056 (mmt) cc_final: 0.7782 (mmt) REVERT: H 489 TYR cc_start: 0.8130 (m-80) cc_final: 0.7475 (m-80) REVERT: I 78 TYR cc_start: 0.8747 (m-80) cc_final: 0.8480 (m-80) REVERT: I 97 TRP cc_start: 0.8319 (t60) cc_final: 0.7800 (t-100) REVERT: I 186 LYS cc_start: 0.8364 (tttp) cc_final: 0.7931 (tptt) REVERT: I 246 ASP cc_start: 0.8737 (t0) cc_final: 0.8406 (t0) REVERT: J 285 ASN cc_start: 0.7027 (m-40) cc_final: 0.6783 (m-40) REVERT: J 305 MET cc_start: 0.8277 (ttt) cc_final: 0.8042 (ttm) REVERT: J 441 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6607 (mt) outliers start: 10 outliers final: 6 residues processed: 432 average time/residue: 0.1833 time to fit residues: 124.4957 Evaluate side-chains 325 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 317 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 441 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.0060 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 30.0000 chunk 298 optimal weight: 0.6980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 48 ASN A 214 GLN A 244 GLN B 116 HIS B 213 ASN C 80 ASN C 138 ASN C 158 HIS C 230 ASN D 44 GLN D 252 HIS D 260 HIS D 277 GLN D 280 ASN D 331 ASN E 41 ASN E 190 HIS E 236 GLN E 283 ASN F 236 GLN G 265 GLN H 265 GLN ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 ASN H 347 GLN H 422 GLN H 448 GLN ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 HIS ** I 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 HIS J 160 ASN J 288 HIS J 337 HIS J 359 ASN J 376 ASN J 440 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.137321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115653 restraints weight = 41757.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.115819 restraints weight = 45095.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.117428 restraints weight = 35857.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.117155 restraints weight = 24605.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.117354 restraints weight = 24431.869| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28003 Z= 0.157 Angle : 0.671 11.271 38025 Z= 0.344 Chirality : 0.046 0.202 4497 Planarity : 0.005 0.078 4909 Dihedral : 5.620 33.358 3934 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.14 % Favored : 91.75 % Rotamer: Outliers : 2.29 % Allowed : 17.26 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.13), residues: 3610 helix: -0.65 (0.14), residues: 1315 sheet: -3.86 (0.19), residues: 531 loop : -3.21 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 136 TYR 0.020 0.002 TYR F 38 PHE 0.032 0.002 PHE E 67 TRP 0.015 0.001 TRP E 37 HIS 0.006 0.001 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00356 (28003) covalent geometry : angle 0.67088 (38025) hydrogen bonds : bond 0.04273 ( 1056) hydrogen bonds : angle 5.22006 ( 3003) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 407 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 MET cc_start: 0.7136 (tpp) cc_final: 0.6746 (tpp) REVERT: C 44 GLN cc_start: 0.8015 (tt0) cc_final: 0.7630 (tt0) REVERT: C 68 MET cc_start: 0.7462 (mtt) cc_final: 0.7083 (mtt) REVERT: C 208 SER cc_start: 0.8085 (t) cc_final: 0.7857 (p) REVERT: D 32 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8277 (tm-30) REVERT: D 139 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7696 (tm-30) REVERT: D 184 LYS cc_start: 0.8300 (mmmt) cc_final: 0.7682 (tptt) REVERT: D 203 MET cc_start: 0.8195 (ttt) cc_final: 0.7826 (ttt) REVERT: E 210 TYR cc_start: 0.8021 (p90) cc_final: 0.6799 (t80) REVERT: E 289 ARG cc_start: 0.6463 (tmt170) cc_final: 0.5832 (tpt170) REVERT: F 172 ASN cc_start: 0.7614 (m-40) cc_final: 0.7244 (m-40) REVERT: G 195 PHE cc_start: 0.7039 (m-80) cc_final: 0.6437 (m-80) REVERT: G 362 ASP cc_start: 0.8655 (t0) cc_final: 0.8400 (t0) REVERT: G 386 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7927 (pp) REVERT: H 489 TYR cc_start: 0.8007 (m-80) cc_final: 0.7419 (m-80) REVERT: I 186 LYS cc_start: 0.8041 (tttp) cc_final: 0.7567 (tptt) REVERT: I 246 ASP cc_start: 0.8640 (t0) cc_final: 0.8433 (t0) REVERT: J 94 PHE cc_start: 0.8222 (m-10) cc_final: 0.7936 (m-10) REVERT: J 368 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8474 (mt) REVERT: J 441 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6664 (mm) outliers start: 65 outliers final: 38 residues processed: 452 average time/residue: 0.1511 time to fit residues: 114.9484 Evaluate side-chains 370 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 329 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 304 HIS Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 348 VAL Chi-restraints excluded: chain J residue 368 ILE Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 449 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 336 optimal weight: 2.9990 chunk 302 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 343 optimal weight: 2.9990 chunk 145 optimal weight: 0.1980 chunk 262 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 HIS ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 GLN G 190 ASN ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 248 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.135793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114428 restraints weight = 42131.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.114453 restraints weight = 49199.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.115804 restraints weight = 38895.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.115953 restraints weight = 27894.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.116168 restraints weight = 27110.350| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 28003 Z= 0.197 Angle : 0.676 9.933 38025 Z= 0.344 Chirality : 0.047 0.181 4497 Planarity : 0.005 0.076 4909 Dihedral : 5.552 36.717 3934 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.03 % Favored : 89.86 % Rotamer: Outliers : 3.48 % Allowed : 20.39 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.13), residues: 3610 helix: -0.25 (0.14), residues: 1317 sheet: -3.42 (0.22), residues: 411 loop : -3.03 (0.13), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 354 TYR 0.023 0.002 TYR J 266 PHE 0.043 0.002 PHE E 67 TRP 0.013 0.001 TRP E 37 HIS 0.006 0.001 HIS G 479 Details of bonding type rmsd covalent geometry : bond 0.00478 (28003) covalent geometry : angle 0.67566 (38025) hydrogen bonds : bond 0.04145 ( 1056) hydrogen bonds : angle 5.01432 ( 3003) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 353 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.6745 (mmm) cc_final: 0.6216 (mtt) REVERT: A 208 ASN cc_start: 0.7686 (t0) cc_final: 0.7422 (t0) REVERT: B 14 MET cc_start: 0.6976 (tpp) cc_final: 0.6415 (tpp) REVERT: B 236 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8652 (m) REVERT: C 32 GLU cc_start: 0.7905 (tt0) cc_final: 0.7620 (tt0) REVERT: C 44 GLN cc_start: 0.7985 (tt0) cc_final: 0.7572 (mt0) REVERT: C 208 SER cc_start: 0.8065 (t) cc_final: 0.7857 (p) REVERT: D 32 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8192 (tm-30) REVERT: D 135 GLU cc_start: 0.7800 (tp30) cc_final: 0.7573 (tp30) REVERT: D 139 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7669 (tm-30) REVERT: D 184 LYS cc_start: 0.8310 (mmmt) cc_final: 0.7656 (tptt) REVERT: D 203 MET cc_start: 0.8231 (ttt) cc_final: 0.7921 (ttt) REVERT: D 217 MET cc_start: 0.7017 (ptt) cc_final: 0.6710 (ptt) REVERT: E 1 MET cc_start: 0.6761 (tpp) cc_final: 0.6355 (tpp) REVERT: E 92 TYR cc_start: 0.7896 (t80) cc_final: 0.7571 (t80) REVERT: E 100 ASP cc_start: 0.7981 (t0) cc_final: 0.7726 (m-30) REVERT: E 116 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7530 (tt0) REVERT: E 176 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6125 (pp) REVERT: E 210 TYR cc_start: 0.7978 (p90) cc_final: 0.6776 (t80) REVERT: E 289 ARG cc_start: 0.6735 (tmt170) cc_final: 0.5975 (tpt170) REVERT: F 172 ASN cc_start: 0.7761 (t0) cc_final: 0.7336 (m-40) REVERT: G 167 VAL cc_start: 0.8707 (t) cc_final: 0.8359 (m) REVERT: G 195 PHE cc_start: 0.7031 (m-80) cc_final: 0.6436 (m-80) REVERT: G 362 ASP cc_start: 0.8665 (t0) cc_final: 0.8444 (t0) REVERT: G 386 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8098 (pp) REVERT: H 229 LEU cc_start: 0.8830 (tp) cc_final: 0.8492 (tp) REVERT: I 106 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8698 (tt) REVERT: I 186 LYS cc_start: 0.8006 (tttp) cc_final: 0.7606 (tptt) REVERT: I 246 ASP cc_start: 0.8657 (t0) cc_final: 0.8415 (t0) REVERT: J 94 PHE cc_start: 0.8220 (m-10) cc_final: 0.7945 (m-10) REVERT: J 368 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8530 (mt) REVERT: J 441 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.6682 (mm) outliers start: 99 outliers final: 66 residues processed: 421 average time/residue: 0.1514 time to fit residues: 108.1809 Evaluate side-chains 392 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 319 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 485 LEU Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 250 SER Chi-restraints excluded: chain J residue 304 HIS Chi-restraints excluded: chain J residue 313 VAL Chi-restraints excluded: chain J residue 348 VAL Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 368 ILE Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 443 LEU Chi-restraints excluded: chain J residue 449 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 43 optimal weight: 0.6980 chunk 257 optimal weight: 0.7980 chunk 303 optimal weight: 4.9990 chunk 334 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 162 optimal weight: 0.5980 chunk 301 optimal weight: 2.9990 chunk 317 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 354 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN B 156 GLN G 213 GLN ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 452 HIS J 384 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.138406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.116795 restraints weight = 41476.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.116642 restraints weight = 47389.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118142 restraints weight = 37125.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118117 restraints weight = 26253.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118325 restraints weight = 25588.131| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28003 Z= 0.147 Angle : 0.633 9.769 38025 Z= 0.320 Chirality : 0.045 0.210 4497 Planarity : 0.004 0.074 4909 Dihedral : 5.337 36.545 3934 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.65 % Favored : 92.24 % Rotamer: Outliers : 3.73 % Allowed : 21.62 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.14), residues: 3610 helix: 0.10 (0.14), residues: 1322 sheet: -3.21 (0.23), residues: 422 loop : -2.79 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 147 TYR 0.018 0.002 TYR D 337 PHE 0.023 0.001 PHE J 264 TRP 0.013 0.001 TRP E 37 HIS 0.005 0.001 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00353 (28003) covalent geometry : angle 0.63292 (38025) hydrogen bonds : bond 0.03750 ( 1056) hydrogen bonds : angle 4.77390 ( 3003) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 354 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.6784 (mmm) cc_final: 0.6457 (mtt) REVERT: B 14 MET cc_start: 0.6479 (tpp) cc_final: 0.5879 (tpp) REVERT: C 22 LEU cc_start: 0.8070 (tp) cc_final: 0.7834 (tp) REVERT: C 32 GLU cc_start: 0.7787 (tt0) cc_final: 0.7508 (tt0) REVERT: C 42 LEU cc_start: 0.8749 (mt) cc_final: 0.8462 (tp) REVERT: C 44 GLN cc_start: 0.7873 (tt0) cc_final: 0.7461 (mt0) REVERT: C 262 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.8354 (t) REVERT: D 32 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8139 (tm-30) REVERT: D 68 MET cc_start: 0.8413 (mmm) cc_final: 0.7540 (mtt) REVERT: D 135 GLU cc_start: 0.7761 (tp30) cc_final: 0.7534 (tp30) REVERT: D 139 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7590 (tm-30) REVERT: D 184 LYS cc_start: 0.8117 (mmmt) cc_final: 0.7447 (tptt) REVERT: D 203 MET cc_start: 0.8150 (ttt) cc_final: 0.7783 (ttt) REVERT: D 217 MET cc_start: 0.6970 (ptt) cc_final: 0.6637 (ptt) REVERT: E 1 MET cc_start: 0.6143 (tpp) cc_final: 0.5802 (tpp) REVERT: E 78 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7768 (mp) REVERT: E 92 TYR cc_start: 0.7889 (t80) cc_final: 0.7622 (t80) REVERT: E 116 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7120 (tt0) REVERT: E 170 MET cc_start: 0.5150 (ptt) cc_final: 0.4947 (ptt) REVERT: E 176 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6086 (pp) REVERT: E 210 TYR cc_start: 0.7928 (p90) cc_final: 0.6693 (t80) REVERT: E 216 MET cc_start: 0.7589 (tpp) cc_final: 0.7225 (tpt) REVERT: E 278 TYR cc_start: 0.5134 (m-80) cc_final: 0.4860 (m-10) REVERT: E 289 ARG cc_start: 0.6612 (tmt170) cc_final: 0.5987 (tpt170) REVERT: F 131 LEU cc_start: 0.9082 (tp) cc_final: 0.8843 (tt) REVERT: F 172 ASN cc_start: 0.7810 (t0) cc_final: 0.7308 (m-40) REVERT: G 167 VAL cc_start: 0.8806 (t) cc_final: 0.8475 (m) REVERT: G 195 PHE cc_start: 0.6926 (m-80) cc_final: 0.6359 (m-80) REVERT: G 362 ASP cc_start: 0.8600 (t0) cc_final: 0.8324 (t0) REVERT: G 386 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8044 (pp) REVERT: G 461 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.7985 (m-30) REVERT: I 106 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8624 (tt) REVERT: I 181 MET cc_start: 0.7535 (ttp) cc_final: 0.7301 (ttp) REVERT: I 186 LYS cc_start: 0.7966 (tttp) cc_final: 0.7520 (tptt) REVERT: J 94 PHE cc_start: 0.8210 (m-10) cc_final: 0.7973 (m-10) REVERT: J 368 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8398 (mt) REVERT: J 441 ILE cc_start: 0.6958 (OUTLIER) cc_final: 0.6618 (mm) outliers start: 106 outliers final: 64 residues processed: 432 average time/residue: 0.1499 time to fit residues: 110.0590 Evaluate side-chains 404 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 331 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 461 ASP Chi-restraints excluded: chain G residue 490 ASP Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 437 CYS Chi-restraints excluded: chain H residue 485 LEU Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 250 SER Chi-restraints excluded: chain J residue 348 VAL Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 368 ILE Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 449 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 94 optimal weight: 0.9990 chunk 347 optimal weight: 20.0000 chunk 336 optimal weight: 0.7980 chunk 259 optimal weight: 0.0670 chunk 32 optimal weight: 5.9990 chunk 210 optimal weight: 0.7980 chunk 354 optimal weight: 5.9990 chunk 350 optimal weight: 0.5980 chunk 248 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 358 optimal weight: 9.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 274 HIS H 274 HIS H 406 HIS ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 288 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.140147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.118733 restraints weight = 41235.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.118449 restraints weight = 45898.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.119934 restraints weight = 36430.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.119800 restraints weight = 26550.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.120064 restraints weight = 23413.553| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28003 Z= 0.132 Angle : 0.608 9.032 38025 Z= 0.308 Chirality : 0.045 0.187 4497 Planarity : 0.004 0.071 4909 Dihedral : 5.085 35.910 3934 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.37 % Favored : 92.52 % Rotamer: Outliers : 3.97 % Allowed : 22.26 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.14), residues: 3610 helix: 0.36 (0.15), residues: 1323 sheet: -3.02 (0.23), residues: 444 loop : -2.58 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 228 TYR 0.015 0.001 TYR D 337 PHE 0.019 0.001 PHE D 177 TRP 0.012 0.001 TRP E 37 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00311 (28003) covalent geometry : angle 0.60834 (38025) hydrogen bonds : bond 0.03506 ( 1056) hydrogen bonds : angle 4.58091 ( 3003) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 379 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.6700 (mmm) cc_final: 0.6172 (mtp) REVERT: B 14 MET cc_start: 0.6186 (tpp) cc_final: 0.5404 (mpp) REVERT: B 243 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7311 (mm-40) REVERT: C 44 GLN cc_start: 0.7880 (tt0) cc_final: 0.7654 (tt0) REVERT: D 32 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8037 (tm-30) REVERT: D 68 MET cc_start: 0.8346 (mmm) cc_final: 0.7564 (mtt) REVERT: D 91 GLU cc_start: 0.7427 (tp30) cc_final: 0.7073 (mt-10) REVERT: D 125 HIS cc_start: 0.4974 (OUTLIER) cc_final: 0.1966 (p90) REVERT: D 135 GLU cc_start: 0.7792 (tp30) cc_final: 0.7588 (tp30) REVERT: D 139 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7778 (tm-30) REVERT: D 184 LYS cc_start: 0.8082 (mmmt) cc_final: 0.7455 (tptt) REVERT: D 203 MET cc_start: 0.8089 (ttt) cc_final: 0.7732 (ttt) REVERT: D 217 MET cc_start: 0.6881 (ptt) cc_final: 0.6621 (ptt) REVERT: E 1 MET cc_start: 0.5989 (tpp) cc_final: 0.5620 (tpp) REVERT: E 92 TYR cc_start: 0.8072 (t80) cc_final: 0.7736 (t80) REVERT: E 116 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7367 (tt0) REVERT: E 176 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6064 (pp) REVERT: E 210 TYR cc_start: 0.8004 (p90) cc_final: 0.6735 (t80) REVERT: E 278 TYR cc_start: 0.5288 (m-80) cc_final: 0.4982 (m-10) REVERT: E 289 ARG cc_start: 0.6602 (tmt170) cc_final: 0.5980 (tpt170) REVERT: F 131 LEU cc_start: 0.9096 (tp) cc_final: 0.8855 (tt) REVERT: F 172 ASN cc_start: 0.7879 (t0) cc_final: 0.7368 (m-40) REVERT: G 167 VAL cc_start: 0.8743 (t) cc_final: 0.8340 (m) REVERT: G 195 PHE cc_start: 0.6911 (m-80) cc_final: 0.6319 (m-80) REVERT: G 265 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8113 (mm-40) REVERT: G 362 ASP cc_start: 0.8636 (t0) cc_final: 0.8401 (t0) REVERT: G 386 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8013 (pp) REVERT: G 461 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8217 (m-30) REVERT: H 260 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7869 (mmm) REVERT: I 106 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8561 (tt) REVERT: I 181 MET cc_start: 0.7482 (ttp) cc_final: 0.7271 (ttp) REVERT: I 186 LYS cc_start: 0.7875 (tttp) cc_final: 0.7459 (tptt) REVERT: I 229 SER cc_start: 0.8942 (p) cc_final: 0.8606 (t) REVERT: I 355 ILE cc_start: 0.8949 (mm) cc_final: 0.8564 (mp) REVERT: J 94 PHE cc_start: 0.8234 (m-10) cc_final: 0.7742 (m-10) REVERT: J 368 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8327 (mt) REVERT: J 441 ILE cc_start: 0.6797 (OUTLIER) cc_final: 0.6505 (mm) outliers start: 113 outliers final: 71 residues processed: 455 average time/residue: 0.1559 time to fit residues: 118.9131 Evaluate side-chains 420 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 340 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 461 ASP Chi-restraints excluded: chain G residue 490 ASP Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 437 CYS Chi-restraints excluded: chain H residue 485 LEU Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 250 SER Chi-restraints excluded: chain J residue 348 VAL Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 368 ILE Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 449 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 145 optimal weight: 0.0770 chunk 154 optimal weight: 40.0000 chunk 6 optimal weight: 0.0980 chunk 284 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 332 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 360 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 chunk 296 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 ASN ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.140813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.119559 restraints weight = 41089.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.119360 restraints weight = 44184.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.120843 restraints weight = 34957.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.120825 restraints weight = 25489.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.120983 restraints weight = 24889.762| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28003 Z= 0.129 Angle : 0.609 9.640 38025 Z= 0.307 Chirality : 0.045 0.224 4497 Planarity : 0.004 0.066 4909 Dihedral : 4.928 35.414 3934 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.93 % Favored : 92.96 % Rotamer: Outliers : 3.69 % Allowed : 22.64 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.14), residues: 3610 helix: 0.57 (0.15), residues: 1321 sheet: -2.97 (0.23), residues: 439 loop : -2.41 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 24 TYR 0.015 0.001 TYR J 128 PHE 0.019 0.001 PHE D 278 TRP 0.013 0.001 TRP E 37 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00305 (28003) covalent geometry : angle 0.60925 (38025) hydrogen bonds : bond 0.03412 ( 1056) hydrogen bonds : angle 4.47794 ( 3003) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 360 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.6666 (mmm) cc_final: 0.6250 (mtp) REVERT: B 14 MET cc_start: 0.6089 (tpp) cc_final: 0.5388 (tpp) REVERT: B 93 MET cc_start: 0.6663 (mmp) cc_final: 0.6271 (mmm) REVERT: B 243 GLN cc_start: 0.7761 (mm-40) cc_final: 0.7269 (mm-40) REVERT: C 44 GLN cc_start: 0.7854 (tt0) cc_final: 0.7581 (tt0) REVERT: D 32 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7966 (tm-30) REVERT: D 68 MET cc_start: 0.8302 (mmm) cc_final: 0.7580 (mtt) REVERT: D 125 HIS cc_start: 0.5179 (OUTLIER) cc_final: 0.2351 (p90) REVERT: D 135 GLU cc_start: 0.7766 (tp30) cc_final: 0.7563 (tp30) REVERT: D 139 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7791 (tm-30) REVERT: D 143 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7475 (tm-30) REVERT: D 184 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7486 (tptt) REVERT: D 203 MET cc_start: 0.8043 (ttt) cc_final: 0.7719 (ttt) REVERT: D 217 MET cc_start: 0.6859 (ptt) cc_final: 0.6523 (ptt) REVERT: E 1 MET cc_start: 0.5812 (tpp) cc_final: 0.5592 (tpp) REVERT: E 92 TYR cc_start: 0.8156 (t80) cc_final: 0.7755 (t80) REVERT: E 116 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7067 (tt0) REVERT: E 176 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6082 (pp) REVERT: E 210 TYR cc_start: 0.7957 (p90) cc_final: 0.6703 (t80) REVERT: E 289 ARG cc_start: 0.6597 (tmt170) cc_final: 0.5921 (tpt170) REVERT: F 131 LEU cc_start: 0.9093 (tp) cc_final: 0.8854 (tt) REVERT: F 172 ASN cc_start: 0.7750 (t0) cc_final: 0.7253 (m-40) REVERT: G 167 VAL cc_start: 0.8777 (t) cc_final: 0.8386 (m) REVERT: G 195 PHE cc_start: 0.6774 (m-80) cc_final: 0.6158 (m-80) REVERT: G 386 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7967 (pp) REVERT: G 461 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8114 (m-30) REVERT: H 260 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7821 (mmm) REVERT: H 459 ASP cc_start: 0.7320 (t70) cc_final: 0.7112 (t0) REVERT: I 106 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8482 (tt) REVERT: I 181 MET cc_start: 0.7510 (ttp) cc_final: 0.7279 (ttp) REVERT: I 186 LYS cc_start: 0.7820 (tttp) cc_final: 0.7419 (tptt) REVERT: I 229 SER cc_start: 0.8722 (p) cc_final: 0.8236 (t) REVERT: I 355 ILE cc_start: 0.9000 (mm) cc_final: 0.8635 (mp) REVERT: J 92 PHE cc_start: 0.7936 (m-80) cc_final: 0.7717 (m-10) REVERT: J 368 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8307 (mt) REVERT: J 441 ILE cc_start: 0.6766 (OUTLIER) cc_final: 0.6505 (mm) outliers start: 105 outliers final: 72 residues processed: 436 average time/residue: 0.1459 time to fit residues: 108.2762 Evaluate side-chains 407 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 326 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 461 ASP Chi-restraints excluded: chain G residue 490 ASP Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 245 ASN Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 437 CYS Chi-restraints excluded: chain H residue 485 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 348 VAL Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 368 ILE Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 449 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 9 optimal weight: 0.9980 chunk 216 optimal weight: 0.9990 chunk 326 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 242 optimal weight: 3.9990 chunk 199 optimal weight: 0.5980 chunk 133 optimal weight: 0.0980 chunk 306 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 301 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 HIS ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 ASN ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 376 ASN ** 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 = 0.3839 r_free = 0.3839 target = 0.141624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.120537 restraints weight = 40873.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.120302 restraints weight = 44755.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122475 restraints weight = 35192.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121974 restraints weight = 25876.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.122348 restraints weight = 23927.037| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28003 Z= 0.129 Angle : 0.609 10.297 38025 Z= 0.308 Chirality : 0.045 0.202 4497 Planarity : 0.004 0.066 4909 Dihedral : 4.852 34.659 3934 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.95 % Favored : 92.94 % Rotamer: Outliers : 4.22 % Allowed : 22.61 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.14), residues: 3610 helix: 0.70 (0.15), residues: 1323 sheet: -2.83 (0.22), residues: 481 loop : -2.32 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 136 TYR 0.018 0.001 TYR J 266 PHE 0.021 0.001 PHE F 237 TRP 0.012 0.001 TRP E 37 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00305 (28003) covalent geometry : angle 0.60901 (38025) hydrogen bonds : bond 0.03360 ( 1056) hydrogen bonds : angle 4.41991 ( 3003) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 342 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.6701 (mmt) cc_final: 0.6403 (mmt) REVERT: A 93 MET cc_start: 0.6395 (mmm) cc_final: 0.6030 (mtp) REVERT: B 243 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7293 (mm-40) REVERT: C 44 GLN cc_start: 0.7781 (tt0) cc_final: 0.7555 (tt0) REVERT: D 32 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7960 (tm-30) REVERT: D 68 MET cc_start: 0.8513 (mmm) cc_final: 0.7925 (mtt) REVERT: D 125 HIS cc_start: 0.5569 (OUTLIER) cc_final: 0.2759 (p90) REVERT: D 135 GLU cc_start: 0.7771 (tp30) cc_final: 0.7567 (tp30) REVERT: D 139 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7787 (tm-30) REVERT: D 143 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7480 (tm-30) REVERT: D 184 LYS cc_start: 0.8099 (mmmt) cc_final: 0.7492 (tptt) REVERT: D 203 MET cc_start: 0.8030 (ttt) cc_final: 0.7694 (ttt) REVERT: D 217 MET cc_start: 0.6658 (ptt) cc_final: 0.6366 (ptt) REVERT: E 1 MET cc_start: 0.5830 (tpp) cc_final: 0.5426 (tpp) REVERT: E 92 TYR cc_start: 0.8127 (t80) cc_final: 0.7599 (t80) REVERT: E 116 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7054 (tt0) REVERT: E 176 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6096 (pp) REVERT: E 210 TYR cc_start: 0.7945 (p90) cc_final: 0.6540 (t80) REVERT: E 289 ARG cc_start: 0.6576 (tmt170) cc_final: 0.5892 (tpt170) REVERT: F 131 LEU cc_start: 0.9105 (tp) cc_final: 0.8882 (tt) REVERT: F 172 ASN cc_start: 0.7760 (t0) cc_final: 0.7335 (m-40) REVERT: G 167 VAL cc_start: 0.8769 (t) cc_final: 0.8393 (m) REVERT: G 195 PHE cc_start: 0.6718 (m-80) cc_final: 0.6111 (m-80) REVERT: G 252 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7768 (tp) REVERT: G 362 ASP cc_start: 0.8731 (t0) cc_final: 0.8502 (t0) REVERT: G 386 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8013 (pp) REVERT: G 461 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8083 (m-30) REVERT: H 260 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7808 (mmm) REVERT: H 459 ASP cc_start: 0.7326 (t70) cc_final: 0.7096 (t0) REVERT: I 106 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8483 (tt) REVERT: I 229 SER cc_start: 0.8548 (p) cc_final: 0.8087 (t) REVERT: I 355 ILE cc_start: 0.9011 (mm) cc_final: 0.8663 (mp) REVERT: J 441 ILE cc_start: 0.6771 (mt) cc_final: 0.6510 (mm) outliers start: 120 outliers final: 84 residues processed: 431 average time/residue: 0.1492 time to fit residues: 109.9788 Evaluate side-chains 415 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 323 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 461 ASP Chi-restraints excluded: chain G residue 490 ASP Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 437 CYS Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 250 SER Chi-restraints excluded: chain J residue 348 VAL Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 449 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 183 optimal weight: 30.0000 chunk 267 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 242 optimal weight: 0.4980 chunk 226 optimal weight: 0.5980 chunk 195 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 HIS ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 GLN ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 376 ASN ** 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 = 0.3827 r_free = 0.3827 target = 0.140746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.123760 restraints weight = 41029.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.123366 restraints weight = 52413.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.123940 restraints weight = 43387.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.123466 restraints weight = 32762.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.124130 restraints weight = 31070.142| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28003 Z= 0.145 Angle : 0.625 10.817 38025 Z= 0.314 Chirality : 0.045 0.187 4497 Planarity : 0.004 0.067 4909 Dihedral : 4.826 34.961 3932 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.42 % Favored : 92.47 % Rotamer: Outliers : 3.87 % Allowed : 23.28 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.14), residues: 3610 helix: 0.71 (0.15), residues: 1325 sheet: -2.74 (0.23), residues: 469 loop : -2.29 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 136 TYR 0.016 0.001 TYR J 128 PHE 0.020 0.002 PHE D 177 TRP 0.011 0.001 TRP F 282 HIS 0.020 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00350 (28003) covalent geometry : angle 0.62473 (38025) hydrogen bonds : bond 0.03450 ( 1056) hydrogen bonds : angle 4.42961 ( 3003) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 343 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.6682 (mmt) cc_final: 0.6395 (mmt) REVERT: A 93 MET cc_start: 0.6399 (mmm) cc_final: 0.6023 (mtp) REVERT: B 243 GLN cc_start: 0.7727 (mm-40) cc_final: 0.7378 (mm-40) REVERT: C 44 GLN cc_start: 0.7767 (tt0) cc_final: 0.7549 (tt0) REVERT: D 32 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7935 (tm-30) REVERT: D 68 MET cc_start: 0.8501 (mmm) cc_final: 0.7998 (mtt) REVERT: D 125 HIS cc_start: 0.5495 (OUTLIER) cc_final: 0.2623 (p90) REVERT: D 139 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7728 (tm-30) REVERT: D 143 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7511 (tm-30) REVERT: D 184 LYS cc_start: 0.8100 (mmmt) cc_final: 0.7528 (tptt) REVERT: D 203 MET cc_start: 0.8020 (ttt) cc_final: 0.7694 (ttt) REVERT: D 217 MET cc_start: 0.6650 (ptt) cc_final: 0.6322 (ptt) REVERT: E 1 MET cc_start: 0.5825 (tpp) cc_final: 0.4963 (tpt) REVERT: E 92 TYR cc_start: 0.7946 (t80) cc_final: 0.7476 (t80) REVERT: E 116 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.6998 (tt0) REVERT: E 176 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6286 (pp) REVERT: E 210 TYR cc_start: 0.7898 (p90) cc_final: 0.6616 (t80) REVERT: E 289 ARG cc_start: 0.6615 (tmt170) cc_final: 0.6139 (tpt170) REVERT: F 131 LEU cc_start: 0.9055 (tp) cc_final: 0.8841 (tt) REVERT: F 172 ASN cc_start: 0.7520 (t0) cc_final: 0.7074 (m-40) REVERT: G 167 VAL cc_start: 0.8669 (t) cc_final: 0.8290 (m) REVERT: G 195 PHE cc_start: 0.6706 (m-80) cc_final: 0.6085 (m-80) REVERT: G 362 ASP cc_start: 0.8659 (t0) cc_final: 0.8458 (t0) REVERT: G 386 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8103 (pp) REVERT: G 461 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8038 (m-30) REVERT: H 260 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7821 (mmm) REVERT: H 459 ASP cc_start: 0.7324 (t70) cc_final: 0.6968 (t0) REVERT: I 106 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8499 (tt) REVERT: I 186 LYS cc_start: 0.7793 (tttp) cc_final: 0.7407 (tptt) REVERT: I 229 SER cc_start: 0.8430 (p) cc_final: 0.7947 (t) REVERT: I 355 ILE cc_start: 0.9005 (mm) cc_final: 0.8671 (mp) REVERT: J 181 MET cc_start: 0.7153 (ttt) cc_final: 0.6792 (ttt) REVERT: J 441 ILE cc_start: 0.6839 (OUTLIER) cc_final: 0.6553 (mm) outliers start: 110 outliers final: 81 residues processed: 423 average time/residue: 0.1472 time to fit residues: 106.3885 Evaluate side-chains 415 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 326 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 461 ASP Chi-restraints excluded: chain G residue 490 ASP Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 437 CYS Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 250 SER Chi-restraints excluded: chain J residue 348 VAL Chi-restraints excluded: chain J residue 370 SER Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 449 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 193 optimal weight: 3.9990 chunk 302 optimal weight: 0.1980 chunk 86 optimal weight: 0.0670 chunk 146 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 315 optimal weight: 4.9990 chunk 162 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 353 optimal weight: 5.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 HIS ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 376 ASN ** 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 = 0.3801 r_free = 0.3801 target = 0.138545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.117476 restraints weight = 41521.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.117806 restraints weight = 44878.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.119010 restraints weight = 35502.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.118892 restraints weight = 25660.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.118979 restraints weight = 26096.054| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 28003 Z= 0.188 Angle : 0.663 10.132 38025 Z= 0.335 Chirality : 0.046 0.179 4497 Planarity : 0.005 0.065 4909 Dihedral : 4.999 36.626 3931 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.75 % Favored : 91.14 % Rotamer: Outliers : 3.80 % Allowed : 23.66 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.14), residues: 3610 helix: 0.62 (0.15), residues: 1326 sheet: -2.79 (0.23), residues: 460 loop : -2.32 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 136 TYR 0.023 0.002 TYR G 214 PHE 0.032 0.002 PHE E 237 TRP 0.010 0.001 TRP E 37 HIS 0.005 0.001 HIS H 204 Details of bonding type rmsd covalent geometry : bond 0.00455 (28003) covalent geometry : angle 0.66281 (38025) hydrogen bonds : bond 0.03632 ( 1056) hydrogen bonds : angle 4.50735 ( 3003) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 330 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ASP cc_start: 0.7335 (t0) cc_final: 0.6924 (m-30) REVERT: A 14 MET cc_start: 0.6372 (mmt) cc_final: 0.6074 (mmt) REVERT: A 93 MET cc_start: 0.6541 (mmm) cc_final: 0.6251 (mtp) REVERT: B 14 MET cc_start: 0.6619 (tpp) cc_final: 0.4617 (mtp) REVERT: B 243 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7472 (mm-40) REVERT: C 42 LEU cc_start: 0.8571 (tp) cc_final: 0.8369 (tp) REVERT: C 44 GLN cc_start: 0.7920 (tt0) cc_final: 0.7703 (tt0) REVERT: D 32 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7976 (tm-30) REVERT: D 68 MET cc_start: 0.8508 (mmm) cc_final: 0.8047 (mtt) REVERT: D 125 HIS cc_start: 0.5417 (OUTLIER) cc_final: 0.5131 (p90) REVERT: D 139 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7728 (tm-30) REVERT: D 184 LYS cc_start: 0.8232 (mmmt) cc_final: 0.7620 (tptt) REVERT: D 203 MET cc_start: 0.8144 (ttt) cc_final: 0.7799 (ttt) REVERT: D 217 MET cc_start: 0.6719 (ptt) cc_final: 0.6402 (ptt) REVERT: E 1 MET cc_start: 0.5875 (tpp) cc_final: 0.5095 (tpp) REVERT: E 92 TYR cc_start: 0.8139 (t80) cc_final: 0.7623 (t80) REVERT: E 176 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6164 (pp) REVERT: E 210 TYR cc_start: 0.7817 (p90) cc_final: 0.6321 (t80) REVERT: E 231 TYR cc_start: 0.8040 (t80) cc_final: 0.7798 (t80) REVERT: E 289 ARG cc_start: 0.6691 (tmt170) cc_final: 0.6130 (tpt170) REVERT: F 131 LEU cc_start: 0.9143 (tp) cc_final: 0.8790 (tt) REVERT: G 461 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8085 (m-30) REVERT: G 490 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7923 (t0) REVERT: G 499 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8048 (mt) REVERT: H 260 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7883 (mmm) REVERT: H 459 ASP cc_start: 0.7536 (t70) cc_final: 0.7190 (t0) REVERT: I 106 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8466 (tt) REVERT: I 186 LYS cc_start: 0.7858 (tttp) cc_final: 0.7478 (tptt) REVERT: I 355 ILE cc_start: 0.9039 (mm) cc_final: 0.8679 (mt) REVERT: J 441 ILE cc_start: 0.6919 (OUTLIER) cc_final: 0.6611 (mm) outliers start: 108 outliers final: 87 residues processed: 410 average time/residue: 0.1485 time to fit residues: 104.1485 Evaluate side-chains 414 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 319 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 461 ASP Chi-restraints excluded: chain G residue 490 ASP Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 437 CYS Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 350 LEU Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 250 SER Chi-restraints excluded: chain J residue 348 VAL Chi-restraints excluded: chain J residue 370 SER Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 431 LEU Chi-restraints excluded: chain J residue 441 ILE Chi-restraints excluded: chain J residue 449 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 113 optimal weight: 0.0870 chunk 267 optimal weight: 2.9990 chunk 360 optimal weight: 0.4980 chunk 249 optimal weight: 1.9990 chunk 188 optimal weight: 30.0000 chunk 344 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 302 optimal weight: 0.1980 chunk 170 optimal weight: 0.7980 chunk 193 optimal weight: 0.6980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 HIS D 162 ASN D 327 ASN ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 411 ASN H 234 GLN ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.142459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121354 restraints weight = 40871.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.121715 restraints weight = 42416.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123167 restraints weight = 32683.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.122951 restraints weight = 23770.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.122985 restraints weight = 23206.065| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28003 Z= 0.124 Angle : 0.626 10.252 38025 Z= 0.313 Chirality : 0.045 0.185 4497 Planarity : 0.004 0.065 4909 Dihedral : 4.778 35.523 3929 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.68 % Favored : 93.21 % Rotamer: Outliers : 3.34 % Allowed : 24.23 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.14), residues: 3610 helix: 0.76 (0.15), residues: 1333 sheet: -2.62 (0.24), residues: 448 loop : -2.20 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 136 TYR 0.020 0.001 TYR A 185 PHE 0.027 0.001 PHE I 465 TRP 0.012 0.001 TRP F 282 HIS 0.015 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00288 (28003) covalent geometry : angle 0.62564 (38025) hydrogen bonds : bond 0.03311 ( 1056) hydrogen bonds : angle 4.40053 ( 3003) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7220 Ramachandran restraints generated. 3610 Oldfield, 0 Emsley, 3610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 341 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3285 (tpp) cc_final: 0.2539 (tpp) REVERT: A 2 ASP cc_start: 0.7323 (t0) cc_final: 0.6985 (m-30) REVERT: A 14 MET cc_start: 0.6618 (mmt) cc_final: 0.6339 (mmt) REVERT: A 20 MET cc_start: 0.5354 (tpp) cc_final: 0.4729 (tpp) REVERT: B 14 MET cc_start: 0.6561 (tpp) cc_final: 0.5983 (mpp) REVERT: B 243 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7363 (mm-40) REVERT: C 44 GLN cc_start: 0.7807 (tt0) cc_final: 0.7580 (tt0) REVERT: D 32 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8057 (tm-30) REVERT: D 68 MET cc_start: 0.8466 (mmm) cc_final: 0.7945 (mtt) REVERT: D 139 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7743 (tm-30) REVERT: D 143 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7535 (tm-30) REVERT: D 184 LYS cc_start: 0.8123 (mmmt) cc_final: 0.7556 (tptt) REVERT: D 203 MET cc_start: 0.8019 (ttt) cc_final: 0.7681 (ttt) REVERT: D 217 MET cc_start: 0.6763 (ptt) cc_final: 0.6428 (ptt) REVERT: E 1 MET cc_start: 0.5772 (tpp) cc_final: 0.4923 (tpt) REVERT: E 92 TYR cc_start: 0.8042 (t80) cc_final: 0.7517 (t80) REVERT: E 116 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7401 (tt0) REVERT: E 176 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6110 (pp) REVERT: E 210 TYR cc_start: 0.7702 (p90) cc_final: 0.6141 (t80) REVERT: E 289 ARG cc_start: 0.6687 (tmt170) cc_final: 0.6151 (tpt170) REVERT: F 28 LEU cc_start: 0.6293 (OUTLIER) cc_final: 0.5831 (tp) REVERT: F 131 LEU cc_start: 0.9149 (tp) cc_final: 0.8798 (tt) REVERT: G 167 VAL cc_start: 0.8962 (t) cc_final: 0.8639 (m) REVERT: G 331 ASP cc_start: 0.8229 (p0) cc_final: 0.7986 (p0) REVERT: G 362 ASP cc_start: 0.8735 (t0) cc_final: 0.8506 (t0) REVERT: G 461 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8077 (m-30) REVERT: G 490 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7855 (t0) REVERT: H 260 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7758 (mmm) REVERT: H 459 ASP cc_start: 0.7446 (t70) cc_final: 0.7199 (t0) REVERT: I 106 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8544 (tt) REVERT: I 229 SER cc_start: 0.8552 (p) cc_final: 0.8129 (t) REVERT: I 355 ILE cc_start: 0.9008 (mm) cc_final: 0.8671 (mp) REVERT: J 441 ILE cc_start: 0.6762 (OUTLIER) cc_final: 0.6512 (mm) outliers start: 95 outliers final: 66 residues processed: 409 average time/residue: 0.1457 time to fit residues: 102.3942 Evaluate side-chains 398 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 324 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 116 HIS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 461 ASP Chi-restraints excluded: chain G residue 490 ASP Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 423 LEU Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 350 LEU Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 250 SER Chi-restraints excluded: chain J residue 348 VAL Chi-restraints excluded: chain J residue 370 SER Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 431 LEU Chi-restraints excluded: chain J residue 441 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 318 optimal weight: 0.7980 chunk 162 optimal weight: 9.9990 chunk 351 optimal weight: 10.0000 chunk 265 optimal weight: 5.9990 chunk 333 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 145 optimal weight: 0.3980 chunk 345 optimal weight: 30.0000 chunk 231 optimal weight: 0.6980 chunk 332 optimal weight: 0.3980 chunk 102 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN B 116 HIS D 162 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 234 GLN ** I 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.142080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.125421 restraints weight = 40737.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.124698 restraints weight = 52183.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.125522 restraints weight = 45066.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.124843 restraints weight = 35781.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.125552 restraints weight = 31426.173| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28003 Z= 0.131 Angle : 0.631 9.666 38025 Z= 0.316 Chirality : 0.045 0.390 4497 Planarity : 0.004 0.066 4909 Dihedral : 4.739 35.667 3929 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.06 % Favored : 92.83 % Rotamer: Outliers : 3.09 % Allowed : 24.89 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.14), residues: 3610 helix: 0.77 (0.15), residues: 1335 sheet: -2.50 (0.24), residues: 444 loop : -2.17 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 155 TYR 0.018 0.001 TYR A 185 PHE 0.027 0.001 PHE F 67 TRP 0.010 0.001 TRP F 282 HIS 0.012 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00313 (28003) covalent geometry : angle 0.63101 (38025) hydrogen bonds : bond 0.03317 ( 1056) hydrogen bonds : angle 4.39401 ( 3003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3733.55 seconds wall clock time: 65 minutes 44.13 seconds (3944.13 seconds total)