Starting phenix.real_space_refine on Sat Aug 23 06:04:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qau_18304/08_2025/8qau_18304.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qau_18304/08_2025/8qau_18304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qau_18304/08_2025/8qau_18304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qau_18304/08_2025/8qau_18304.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qau_18304/08_2025/8qau_18304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qau_18304/08_2025/8qau_18304.map" } resolution = 3.54 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 142 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 59 5.16 5 C 6370 2.51 5 N 1749 2.21 5 O 1953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10137 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3373 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 410} Chain breaks: 1 Chain: "D" Number of atoms: 3359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3359 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1700 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 8, 'TRANS': 244} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 461 Unresolved non-hydrogen angles: 585 Unresolved non-hydrogen dihedrals: 380 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'ASP:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 10, 'GLN:plan1': 11, 'GLU:plan': 14, 'TYR:plan': 8, 'PHE:plan': 4, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 268 Chain: "B" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1440 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 4, 'TRANS': 202} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 11, 'PHE:plan': 3, 'ASP:plan': 7, 'ASN:plan1': 4, 'GLN:plan1': 11, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 168 Chain: "E" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 142 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 4, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.31, per 1000 atoms: 0.23 Number of scatterers: 10137 At special positions: 0 Unit cell: (171.72, 101.76, 118.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 59 16.00 P 5 15.00 Mg 1 11.99 O 1953 8.00 N 1749 7.00 C 6370 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 329.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 5 sheets defined 62.6% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'C' and resid 9 through 28 removed outlier: 3.756A pdb=" N GLN C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.625A pdb=" N ASN C 50 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 47 through 51' Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 114 through 129 removed outlier: 3.790A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 161 removed outlier: 4.336A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 190 Processing helix chain 'C' and resid 190 through 196 removed outlier: 3.947A pdb=" N GLU C 196 " --> pdb=" O HIS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 216 Processing helix chain 'C' and resid 223 through 240 removed outlier: 3.979A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 243 No H-bonds generated for 'chain 'C' and resid 241 through 243' Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.589A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 384 through 400 removed outlier: 3.675A pdb=" N TRP C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP C 396 " --> pdb=" O ASP C 392 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET C 398 " --> pdb=" O LYS C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 415 through 432 removed outlier: 4.001A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS C 430 " --> pdb=" O ALA C 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 46 through 49 Processing helix chain 'D' and resid 69 through 78 removed outlier: 4.627A pdb=" N MET D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.637A pdb=" N ILE D 84 " --> pdb=" O PHE D 81 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE D 85 " --> pdb=" O GLY D 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 81 through 85' Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 109 through 126 removed outlier: 4.230A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 159 Processing helix chain 'D' and resid 180 through 195 removed outlier: 3.536A pdb=" N ASN D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'D' and resid 221 through 237 removed outlier: 3.643A pdb=" N LEU D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 removed outlier: 3.823A pdb=" N ARG D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.739A pdb=" N PHE D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 322 through 337 removed outlier: 3.670A pdb=" N VAL D 326 " --> pdb=" O SER D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 390 removed outlier: 3.601A pdb=" N PHE D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 402 removed outlier: 4.232A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 427 removed outlier: 4.373A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN D 426 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 139 removed outlier: 3.538A pdb=" N ASN A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 158 through 172 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 203 through 209 Processing helix chain 'A' and resid 214 through 255 removed outlier: 5.001A pdb=" N GLY A 220 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU A 250 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ILE A 251 " --> pdb=" O ASN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 292 removed outlier: 3.933A pdb=" N LYS A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 365 Processing helix chain 'B' and resid 12 through 24 removed outlier: 3.855A pdb=" N LEU B 16 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 37 through 53 removed outlier: 4.320A pdb=" N MET B 53 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 70 removed outlier: 3.754A pdb=" N LEU B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLU B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N THR B 68 " --> pdb=" O SER B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 101 Processing helix chain 'B' and resid 107 through 113 removed outlier: 3.774A pdb=" N LEU B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 140 Processing helix chain 'B' and resid 140 through 169 removed outlier: 3.577A pdb=" N ILE B 144 " --> pdb=" O CYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 207 Processing helix chain 'E' and resid 257 through 267 Processing sheet with id=AA1, first strand: chain 'C' and resid 92 through 93 removed outlier: 8.036A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLU C 3 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N SER C 136 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE C 5 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N PHE C 138 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 7 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N SER C 165 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN C 133 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU C 167 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'C' and resid 269 through 273 Processing sheet with id=AA4, first strand: chain 'D' and resid 91 through 92 removed outlier: 7.974A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLU D 3 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY D 132 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N SER D 138 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLN D 131 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ASN D 165 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N PHE D 133 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE D 167 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU D 135 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL D 169 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N HIS D 137 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N MET D 164 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N TYR D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR D 166 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE D 202 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER D 168 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N CYS D 201 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 10.614A pdb=" N PHE D 270 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 14.092A pdb=" N ASP D 203 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 51 through 54 608 hydrogen bonds defined for protein. 1779 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: 1.28 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1818 1.32 - 1.44: 2651 1.44 - 1.57: 5764 1.57 - 1.69: 13 1.69 - 1.81: 94 Bond restraints: 10340 Sorted by residual: bond pdb=" CG PRO C 32 " pdb=" CD PRO C 32 " ideal model delta sigma weight residual 1.503 1.265 0.238 3.40e-02 8.65e+02 4.91e+01 bond pdb=" N PRO C 32 " pdb=" CD PRO C 32 " ideal model delta sigma weight residual 1.473 1.507 -0.034 1.40e-02 5.10e+03 6.02e+00 bond pdb=" CB PRO C 32 " pdb=" CG PRO C 32 " ideal model delta sigma weight residual 1.492 1.597 -0.105 5.00e-02 4.00e+02 4.40e+00 bond pdb=" CG GLU A 131 " pdb=" CD GLU A 131 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.64e+00 bond pdb=" CD GLU A 131 " pdb=" OE1 GLU A 131 " ideal model delta sigma weight residual 1.249 1.225 0.024 1.90e-02 2.77e+03 1.58e+00 ... (remaining 10335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 13986 3.31 - 6.62: 82 6.62 - 9.92: 9 9.92 - 13.23: 0 13.23 - 16.54: 2 Bond angle restraints: 14079 Sorted by residual: angle pdb=" CA PRO C 32 " pdb=" N PRO C 32 " pdb=" CD PRO C 32 " ideal model delta sigma weight residual 112.00 95.46 16.54 1.40e+00 5.10e-01 1.40e+02 angle pdb=" N PRO C 32 " pdb=" CD PRO C 32 " pdb=" CG PRO C 32 " ideal model delta sigma weight residual 103.20 89.05 14.15 1.50e+00 4.44e-01 8.89e+01 angle pdb=" CA PRO C 32 " pdb=" CB PRO C 32 " pdb=" CG PRO C 32 " ideal model delta sigma weight residual 104.50 94.58 9.92 1.90e+00 2.77e-01 2.73e+01 angle pdb=" CA MET B 108 " pdb=" CB MET B 108 " pdb=" CG MET B 108 " ideal model delta sigma weight residual 114.10 121.77 -7.67 2.00e+00 2.50e-01 1.47e+01 angle pdb=" N GLY C 10 " pdb=" CA GLY C 10 " pdb=" C GLY C 10 " ideal model delta sigma weight residual 113.18 122.13 -8.95 2.37e+00 1.78e-01 1.43e+01 ... (remaining 14074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.23: 6038 32.23 - 64.46: 154 64.46 - 96.70: 29 96.70 - 128.93: 5 128.93 - 161.16: 11 Dihedral angle restraints: 6237 sinusoidal: 2318 harmonic: 3919 Sorted by residual: dihedral pdb=" C5' GDP D 501 " pdb=" O5' GDP D 501 " pdb=" PA GDP D 501 " pdb=" O3A GDP D 501 " ideal model delta sinusoidal sigma weight residual 179.98 37.05 142.93 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" CA VAL C 9 " pdb=" C VAL C 9 " pdb=" N GLY C 10 " pdb=" CA GLY C 10 " ideal model delta harmonic sigma weight residual -180.00 -149.55 -30.45 0 5.00e+00 4.00e-02 3.71e+01 dihedral pdb=" C8 GTP C 501 " pdb=" C1' GTP C 501 " pdb=" N9 GTP C 501 " pdb=" O4' GTP C 501 " ideal model delta sinusoidal sigma weight residual 104.59 -10.71 115.31 1 2.00e+01 2.50e-03 3.43e+01 ... (remaining 6234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1293 0.052 - 0.105: 255 0.105 - 0.157: 36 0.157 - 0.209: 3 0.209 - 0.262: 1 Chirality restraints: 1588 Sorted by residual: chirality pdb=" C10 TA1 D 502 " pdb=" C02 TA1 D 502 " pdb=" C11 TA1 D 502 " pdb=" C18 TA1 D 502 " both_signs ideal model delta sigma weight residual False 2.54 2.28 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C02 TA1 D 502 " pdb=" C01 TA1 D 502 " pdb=" C10 TA1 D 502 " pdb=" O02 TA1 D 502 " both_signs ideal model delta sigma weight residual False 2.56 2.75 -0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CA ASN A 146 " pdb=" N ASN A 146 " pdb=" C ASN A 146 " pdb=" CB ASN A 146 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 ... (remaining 1585 not shown) Planarity restraints: 1846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 31 " 0.092 5.00e-02 4.00e+02 1.25e-01 2.50e+01 pdb=" N PRO C 32 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO C 32 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 32 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 76 " 0.009 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" CD GLU B 76 " -0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU B 76 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 76 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 50 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" CD GLU B 50 " 0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU B 50 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 50 " -0.012 2.00e-02 2.50e+03 ... (remaining 1843 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 95 2.56 - 3.15: 8593 3.15 - 3.73: 16539 3.73 - 4.32: 21501 4.32 - 4.90: 35889 Nonbonded interactions: 82617 Sorted by model distance: nonbonded pdb=" OD2 ASP C 98 " pdb="MG MG C 502 " model vdw 1.980 2.170 nonbonded pdb=" O1G GTP C 501 " pdb="MG MG C 502 " model vdw 2.061 2.170 nonbonded pdb=" O3G GTP C 501 " pdb="MG MG C 502 " model vdw 2.152 2.170 nonbonded pdb=" OG SER C 178 " pdb=" OE1 GLU C 183 " model vdw 2.185 3.040 nonbonded pdb=" O ALA D 63 " pdb=" ND2 ASN D 89 " model vdw 2.238 3.120 ... (remaining 82612 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.380 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 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 : 0.004 0.238 10341 Z= 0.161 Angle : 0.690 16.538 14079 Z= 0.365 Chirality : 0.042 0.262 1588 Planarity : 0.005 0.125 1846 Dihedral : 17.836 161.161 3703 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 0.50 (0.23), residues: 1333 helix: 1.34 (0.19), residues: 743 sheet: -0.49 (0.47), residues: 123 loop : -1.03 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 306 TYR 0.014 0.001 TYR C 282 PHE 0.019 0.001 PHE C 49 TRP 0.021 0.002 TRP C 388 HIS 0.004 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00402 (10340) covalent geometry : angle 0.69037 (14079) hydrogen bonds : bond 0.14611 ( 608) hydrogen bonds : angle 6.00362 ( 1779) Misc. bond : bond 0.00331 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 154 MET cc_start: 0.5297 (mmm) cc_final: 0.5087 (mmm) REVERT: C 346 TRP cc_start: 0.6579 (p-90) cc_final: 0.4151 (t60) REVERT: A 225 MET cc_start: 0.8826 (mmp) cc_final: 0.8577 (mtp) REVERT: B 101 ILE cc_start: 0.6545 (pt) cc_final: 0.6278 (pt) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.0906 time to fit residues: 36.6386 Evaluate side-chains 177 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.0370 chunk 55 optimal weight: 0.6980 overall best weight: 2.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 ASN D 105 HIS ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 HIS ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 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 = 0.4010 r_free = 0.4010 target = 0.104662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.075260 restraints weight = 36654.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.077283 restraints weight = 17635.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.078677 restraints weight = 10813.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.079559 restraints weight = 7748.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.080040 restraints weight = 6159.639| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10341 Z= 0.206 Angle : 0.710 8.852 14079 Z= 0.359 Chirality : 0.044 0.193 1588 Planarity : 0.005 0.046 1846 Dihedral : 15.334 144.746 1571 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.47 % Rotamer: Outliers : 2.37 % Allowed : 13.17 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 0.84 (0.23), residues: 1333 helix: 1.59 (0.19), residues: 754 sheet: -0.76 (0.46), residues: 122 loop : -0.76 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 306 TYR 0.024 0.002 TYR B 112 PHE 0.019 0.002 PHE B 97 TRP 0.021 0.002 TRP D 21 HIS 0.006 0.002 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.00448 (10340) covalent geometry : angle 0.70964 (14079) hydrogen bonds : bond 0.04632 ( 608) hydrogen bonds : angle 4.58542 ( 1779) Misc. bond : bond 0.00193 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 MET cc_start: 0.9473 (tmm) cc_final: 0.9067 (tmm) REVERT: C 141 PHE cc_start: 0.9115 (m-10) cc_final: 0.8867 (m-10) REVERT: C 164 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8597 (mmmm) REVERT: C 172 TYR cc_start: 0.8955 (t80) cc_final: 0.8319 (t80) REVERT: C 185 TYR cc_start: 0.9548 (m-80) cc_final: 0.9344 (m-80) REVERT: C 358 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.9052 (tp30) REVERT: D 1 MET cc_start: 0.8442 (mmm) cc_final: 0.8239 (mmm) REVERT: D 74 ASP cc_start: 0.9385 (m-30) cc_final: 0.9050 (p0) REVERT: D 130 LEU cc_start: 0.9107 (tp) cc_final: 0.8631 (tp) REVERT: D 180 VAL cc_start: 0.9319 (m) cc_final: 0.9076 (p) REVERT: D 181 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7864 (mt-10) REVERT: D 190 HIS cc_start: 0.8927 (t-90) cc_final: 0.8671 (t-90) REVERT: D 257 MET cc_start: 0.8839 (mmm) cc_final: 0.8030 (mmt) REVERT: D 265 PHE cc_start: 0.9581 (m-10) cc_final: 0.9330 (m-10) REVERT: D 330 MET cc_start: 0.9065 (mmp) cc_final: 0.8848 (mmm) REVERT: D 375 GLN cc_start: 0.9577 (pm20) cc_final: 0.9291 (pm20) REVERT: D 376 GLU cc_start: 0.9385 (mm-30) cc_final: 0.8996 (mm-30) REVERT: D 379 LYS cc_start: 0.8936 (ptpt) cc_final: 0.8432 (ptpt) REVERT: A 177 TYR cc_start: 0.8159 (t80) cc_final: 0.7608 (t80) outliers start: 23 outliers final: 13 residues processed: 200 average time/residue: 0.0732 time to fit residues: 21.5891 Evaluate side-chains 184 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 316 CYS Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain B residue 39 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 78 optimal weight: 0.2980 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 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 = 0.4030 r_free = 0.4030 target = 0.105041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.075685 restraints weight = 36546.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.077793 restraints weight = 17621.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.079225 restraints weight = 10782.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.080093 restraints weight = 7626.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.080578 restraints weight = 6056.021| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10341 Z= 0.151 Angle : 0.640 10.379 14079 Z= 0.322 Chirality : 0.043 0.249 1588 Planarity : 0.004 0.048 1846 Dihedral : 13.686 141.950 1571 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.93 % Favored : 97.00 % Rotamer: Outliers : 2.16 % Allowed : 16.46 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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 aren not related in a simple way. whole: 1.10 (0.23), residues: 1333 helix: 1.78 (0.19), residues: 757 sheet: -0.34 (0.48), residues: 109 loop : -0.73 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 306 TYR 0.012 0.001 TYR A 188 PHE 0.012 0.001 PHE D 367 TRP 0.028 0.002 TRP D 21 HIS 0.004 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00326 (10340) covalent geometry : angle 0.64032 (14079) hydrogen bonds : bond 0.04132 ( 608) hydrogen bonds : angle 4.33000 ( 1779) Misc. bond : bond 0.00071 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 MET cc_start: 0.9474 (tmm) cc_final: 0.8949 (tmm) REVERT: C 116 ASP cc_start: 0.8930 (p0) cc_final: 0.8597 (p0) REVERT: C 120 ASP cc_start: 0.8694 (m-30) cc_final: 0.8054 (m-30) REVERT: C 141 PHE cc_start: 0.9156 (m-10) cc_final: 0.8946 (m-10) REVERT: C 164 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8732 (mmmm) REVERT: C 358 GLU cc_start: 0.9253 (OUTLIER) cc_final: 0.9017 (tp30) REVERT: C 377 MET cc_start: 0.8315 (tmm) cc_final: 0.7788 (tmm) REVERT: C 380 ASN cc_start: 0.9119 (t0) cc_final: 0.8917 (t0) REVERT: C 413 MET cc_start: 0.8608 (tpp) cc_final: 0.8230 (tpp) REVERT: C 417 GLU cc_start: 0.8617 (tt0) cc_final: 0.8368 (tt0) REVERT: C 425 MET cc_start: 0.9487 (mmm) cc_final: 0.9093 (tpp) REVERT: C 429 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8646 (mm-30) REVERT: D 1 MET cc_start: 0.8437 (mmm) cc_final: 0.8176 (mmm) REVERT: D 74 ASP cc_start: 0.9338 (m-30) cc_final: 0.9093 (m-30) REVERT: D 180 VAL cc_start: 0.9347 (m) cc_final: 0.9120 (p) REVERT: D 181 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7774 (mt-10) REVERT: D 190 HIS cc_start: 0.8854 (t-90) cc_final: 0.8569 (t-90) REVERT: D 257 MET cc_start: 0.8825 (mmm) cc_final: 0.8049 (mmt) REVERT: A 177 TYR cc_start: 0.8246 (t80) cc_final: 0.6953 (t80) REVERT: A 189 GLN cc_start: 0.9234 (tp40) cc_final: 0.8806 (pp30) outliers start: 21 outliers final: 12 residues processed: 195 average time/residue: 0.0868 time to fit residues: 24.7659 Evaluate side-chains 180 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain B residue 39 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 16 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 18 optimal weight: 0.1980 chunk 116 optimal weight: 20.0000 chunk 60 optimal weight: 0.2980 chunk 87 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 107 optimal weight: 30.0000 chunk 102 optimal weight: 20.0000 chunk 71 optimal weight: 0.0770 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 ASN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 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 = 0.4047 r_free = 0.4047 target = 0.106189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.076795 restraints weight = 36676.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.078977 restraints weight = 17648.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.080416 restraints weight = 10726.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.081325 restraints weight = 7591.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.081828 restraints weight = 5987.927| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10341 Z= 0.123 Angle : 0.622 10.760 14079 Z= 0.310 Chirality : 0.043 0.442 1588 Planarity : 0.004 0.046 1846 Dihedral : 9.655 139.651 1571 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.70 % Favored : 97.22 % Rotamer: Outliers : 2.37 % Allowed : 17.28 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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 aren not related in a simple way. whole: 1.29 (0.23), residues: 1333 helix: 1.93 (0.19), residues: 757 sheet: -0.23 (0.48), residues: 109 loop : -0.65 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 221 TYR 0.016 0.001 TYR B 40 PHE 0.018 0.001 PHE A 153 TRP 0.028 0.002 TRP D 21 HIS 0.005 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00267 (10340) covalent geometry : angle 0.62218 (14079) hydrogen bonds : bond 0.03778 ( 608) hydrogen bonds : angle 4.17062 ( 1779) Misc. bond : bond 0.00127 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 MET cc_start: 0.9494 (tmm) cc_final: 0.8956 (tmm) REVERT: C 141 PHE cc_start: 0.9081 (m-10) cc_final: 0.8830 (m-10) REVERT: C 164 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8531 (mtpt) REVERT: C 203 MET cc_start: 0.8763 (mmm) cc_final: 0.8181 (mmm) REVERT: C 377 MET cc_start: 0.8437 (tmm) cc_final: 0.7849 (tmm) REVERT: C 413 MET cc_start: 0.8512 (tpp) cc_final: 0.7892 (tpp) REVERT: C 417 GLU cc_start: 0.8666 (tt0) cc_final: 0.8405 (tt0) REVERT: C 425 MET cc_start: 0.9454 (mmm) cc_final: 0.9030 (tpp) REVERT: C 429 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8666 (mm-30) REVERT: D 1 MET cc_start: 0.8415 (mmm) cc_final: 0.8048 (mmm) REVERT: D 74 ASP cc_start: 0.9314 (m-30) cc_final: 0.9046 (m-30) REVERT: D 147 MET cc_start: 0.9558 (tpp) cc_final: 0.9174 (mmm) REVERT: D 180 VAL cc_start: 0.9405 (m) cc_final: 0.9106 (p) REVERT: D 181 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7792 (mt-10) REVERT: D 190 HIS cc_start: 0.8836 (t-90) cc_final: 0.8543 (t-90) REVERT: D 257 MET cc_start: 0.8786 (mmm) cc_final: 0.7735 (mmt) REVERT: D 262 ARG cc_start: 0.8958 (mtp85) cc_final: 0.8634 (mtm-85) REVERT: A 177 TYR cc_start: 0.8375 (t80) cc_final: 0.8017 (t80) REVERT: A 185 ASN cc_start: 0.9443 (m-40) cc_final: 0.8876 (p0) REVERT: B 58 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8481 (mp0) outliers start: 23 outliers final: 10 residues processed: 201 average time/residue: 0.0899 time to fit residues: 25.8366 Evaluate side-chains 179 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 50 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 88 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 78 optimal weight: 0.0000 chunk 56 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 overall best weight: 4.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 ASN C 372 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.102025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.072481 restraints weight = 38122.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.074336 restraints weight = 18571.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.075662 restraints weight = 11718.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.076501 restraints weight = 8546.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.076922 restraints weight = 6929.698| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10341 Z= 0.300 Angle : 0.739 8.956 14079 Z= 0.380 Chirality : 0.046 0.270 1588 Planarity : 0.004 0.050 1846 Dihedral : 9.444 152.901 1571 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.25 % Rotamer: Outliers : 2.88 % Allowed : 19.96 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 1.11 (0.23), residues: 1333 helix: 1.80 (0.19), residues: 757 sheet: -0.51 (0.45), residues: 125 loop : -0.69 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 380 TYR 0.026 0.002 TYR C 210 PHE 0.017 0.002 PHE D 167 TRP 0.042 0.003 TRP D 21 HIS 0.008 0.002 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00648 (10340) covalent geometry : angle 0.73928 (14079) hydrogen bonds : bond 0.04444 ( 608) hydrogen bonds : angle 4.45343 ( 1779) Misc. bond : bond 0.00261 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 MET cc_start: 0.9590 (tmm) cc_final: 0.9214 (tmm) REVERT: C 116 ASP cc_start: 0.8948 (p0) cc_final: 0.8582 (p0) REVERT: C 120 ASP cc_start: 0.8671 (m-30) cc_final: 0.8031 (m-30) REVERT: C 164 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8685 (mtpt) REVERT: C 377 MET cc_start: 0.8320 (tmm) cc_final: 0.8021 (tmm) REVERT: C 413 MET cc_start: 0.8421 (tpp) cc_final: 0.7708 (tpp) REVERT: C 417 GLU cc_start: 0.8736 (tt0) cc_final: 0.8387 (tt0) REVERT: C 425 MET cc_start: 0.9413 (mmm) cc_final: 0.8884 (tpp) REVERT: D 74 ASP cc_start: 0.9295 (m-30) cc_final: 0.9051 (m-30) REVERT: D 180 VAL cc_start: 0.9442 (m) cc_final: 0.9204 (p) REVERT: D 181 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8122 (mt-10) REVERT: D 257 MET cc_start: 0.8851 (mmm) cc_final: 0.8338 (mmt) REVERT: D 375 GLN cc_start: 0.9460 (pm20) cc_final: 0.9218 (pm20) REVERT: D 407 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8928 (mp0) REVERT: A 177 TYR cc_start: 0.8316 (t80) cc_final: 0.7811 (t80) REVERT: B 58 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8767 (mp0) outliers start: 28 outliers final: 14 residues processed: 187 average time/residue: 0.0734 time to fit residues: 20.1442 Evaluate side-chains 167 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 50 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.0270 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 64 optimal weight: 0.0010 chunk 45 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 110 optimal weight: 20.0000 overall best weight: 0.5044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 249 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN ** B 91 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 = 0.4020 r_free = 0.4020 target = 0.103717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.074439 restraints weight = 36844.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.076446 restraints weight = 17738.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.077889 restraints weight = 10901.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.078824 restraints weight = 7749.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.079343 restraints weight = 6109.670| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10341 Z= 0.124 Angle : 0.639 9.547 14079 Z= 0.324 Chirality : 0.043 0.269 1588 Planarity : 0.004 0.048 1846 Dihedral : 8.976 147.549 1571 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.85 % Favored : 97.07 % Rotamer: Outliers : 1.95 % Allowed : 21.60 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 1.37 (0.24), residues: 1333 helix: 1.96 (0.19), residues: 757 sheet: -0.29 (0.46), residues: 119 loop : -0.51 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 114 TYR 0.021 0.001 TYR B 40 PHE 0.026 0.001 PHE A 153 TRP 0.039 0.002 TRP D 21 HIS 0.006 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00268 (10340) covalent geometry : angle 0.63909 (14079) hydrogen bonds : bond 0.03831 ( 608) hydrogen bonds : angle 4.16524 ( 1779) Misc. bond : bond 0.00310 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 MET cc_start: 0.9561 (tmm) cc_final: 0.9151 (tmm) REVERT: C 116 ASP cc_start: 0.8950 (p0) cc_final: 0.8570 (p0) REVERT: C 120 ASP cc_start: 0.8667 (m-30) cc_final: 0.7975 (m-30) REVERT: C 141 PHE cc_start: 0.9022 (m-10) cc_final: 0.8661 (m-10) REVERT: C 154 MET cc_start: 0.9185 (tpp) cc_final: 0.8904 (mmm) REVERT: C 203 MET cc_start: 0.8904 (mmm) cc_final: 0.8520 (mmm) REVERT: C 377 MET cc_start: 0.8382 (tmm) cc_final: 0.7948 (tmm) REVERT: C 413 MET cc_start: 0.8388 (tpp) cc_final: 0.7615 (tpp) REVERT: C 417 GLU cc_start: 0.8728 (tt0) cc_final: 0.8355 (tt0) REVERT: C 425 MET cc_start: 0.9353 (mmm) cc_final: 0.8953 (tpp) REVERT: C 429 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8452 (mm-30) REVERT: D 74 ASP cc_start: 0.9295 (m-30) cc_final: 0.9067 (m-30) REVERT: D 147 MET cc_start: 0.9555 (tpp) cc_final: 0.9126 (mmm) REVERT: D 180 VAL cc_start: 0.9425 (m) cc_final: 0.9145 (p) REVERT: D 257 MET cc_start: 0.8986 (mmm) cc_final: 0.8335 (mmt) REVERT: D 267 MET cc_start: 0.8867 (mmm) cc_final: 0.8526 (mmt) REVERT: D 285 THR cc_start: 0.9436 (OUTLIER) cc_final: 0.8388 (t) REVERT: D 330 MET cc_start: 0.9068 (mmp) cc_final: 0.8765 (mmm) REVERT: D 376 GLU cc_start: 0.9359 (mm-30) cc_final: 0.9135 (mm-30) REVERT: A 177 TYR cc_start: 0.8302 (t80) cc_final: 0.7935 (t80) REVERT: B 58 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8639 (mp0) outliers start: 19 outliers final: 12 residues processed: 195 average time/residue: 0.0795 time to fit residues: 23.0361 Evaluate side-chains 179 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 50 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 83 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 99 optimal weight: 50.0000 chunk 79 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 71 optimal weight: 0.0980 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 256 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.103393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.074881 restraints weight = 36545.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.076883 restraints weight = 17662.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.078248 restraints weight = 10954.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.079170 restraints weight = 7852.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.079697 restraints weight = 6205.660| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10341 Z= 0.144 Angle : 0.684 17.186 14079 Z= 0.346 Chirality : 0.045 0.304 1588 Planarity : 0.004 0.049 1846 Dihedral : 8.617 148.105 1571 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 2.26 % Allowed : 23.25 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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 aren not related in a simple way. whole: 1.40 (0.24), residues: 1333 helix: 1.96 (0.19), residues: 756 sheet: -0.15 (0.46), residues: 119 loop : -0.49 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 114 TYR 0.025 0.002 TYR C 210 PHE 0.011 0.001 PHE A 198 TRP 0.038 0.002 TRP D 21 HIS 0.004 0.001 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00320 (10340) covalent geometry : angle 0.68363 (14079) hydrogen bonds : bond 0.03839 ( 608) hydrogen bonds : angle 4.15755 ( 1779) Misc. bond : bond 0.00739 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 MET cc_start: 0.9554 (tmm) cc_final: 0.9137 (tmm) REVERT: C 116 ASP cc_start: 0.8920 (p0) cc_final: 0.8561 (p0) REVERT: C 120 ASP cc_start: 0.8670 (m-30) cc_final: 0.7952 (m-30) REVERT: C 154 MET cc_start: 0.9217 (tpp) cc_final: 0.8901 (mmm) REVERT: C 377 MET cc_start: 0.8343 (tmm) cc_final: 0.7961 (tmm) REVERT: C 413 MET cc_start: 0.8361 (tpp) cc_final: 0.7621 (tpp) REVERT: C 417 GLU cc_start: 0.8725 (tt0) cc_final: 0.8360 (tt0) REVERT: C 425 MET cc_start: 0.9282 (mmm) cc_final: 0.8887 (tpp) REVERT: C 429 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8392 (mm-30) REVERT: D 74 ASP cc_start: 0.9278 (m-30) cc_final: 0.9038 (m-30) REVERT: D 147 MET cc_start: 0.9557 (tpp) cc_final: 0.9130 (mmm) REVERT: D 180 VAL cc_start: 0.9440 (m) cc_final: 0.9158 (p) REVERT: D 257 MET cc_start: 0.8956 (mmm) cc_final: 0.8231 (mmt) REVERT: D 330 MET cc_start: 0.9061 (mmp) cc_final: 0.8838 (mmm) REVERT: A 130 GLU cc_start: 0.9409 (mm-30) cc_final: 0.9187 (mm-30) REVERT: A 177 TYR cc_start: 0.8281 (t80) cc_final: 0.7938 (t80) REVERT: B 58 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8705 (mp0) outliers start: 22 outliers final: 12 residues processed: 184 average time/residue: 0.0763 time to fit residues: 20.7561 Evaluate side-chains 175 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 50 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 0.0070 chunk 97 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 117 optimal weight: 30.0000 chunk 22 optimal weight: 2.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN A 214 ASN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.104145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.074702 restraints weight = 36785.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.076832 restraints weight = 17925.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.078244 restraints weight = 11038.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.079194 restraints weight = 7870.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.079717 restraints weight = 6200.994| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10341 Z= 0.135 Angle : 0.675 12.754 14079 Z= 0.342 Chirality : 0.044 0.336 1588 Planarity : 0.004 0.045 1846 Dihedral : 8.417 147.159 1571 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.00 % Favored : 96.92 % Rotamer: Outliers : 1.95 % Allowed : 23.97 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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 aren not related in a simple way. whole: 1.36 (0.24), residues: 1333 helix: 1.93 (0.19), residues: 756 sheet: -0.12 (0.46), residues: 119 loop : -0.52 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 114 TYR 0.024 0.002 TYR B 40 PHE 0.026 0.001 PHE A 153 TRP 0.033 0.002 TRP D 21 HIS 0.009 0.001 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00303 (10340) covalent geometry : angle 0.67495 (14079) hydrogen bonds : bond 0.03750 ( 608) hydrogen bonds : angle 4.16475 ( 1779) Misc. bond : bond 0.00597 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 MET cc_start: 0.9549 (tmm) cc_final: 0.9123 (tmm) REVERT: C 116 ASP cc_start: 0.8912 (p0) cc_final: 0.8540 (p0) REVERT: C 120 ASP cc_start: 0.8679 (m-30) cc_final: 0.7971 (m-30) REVERT: C 141 PHE cc_start: 0.9052 (m-10) cc_final: 0.8698 (m-10) REVERT: C 377 MET cc_start: 0.8332 (tmm) cc_final: 0.7953 (tmm) REVERT: C 413 MET cc_start: 0.8314 (tpp) cc_final: 0.7566 (tpp) REVERT: C 417 GLU cc_start: 0.8723 (tt0) cc_final: 0.8358 (tt0) REVERT: C 425 MET cc_start: 0.9295 (mmm) cc_final: 0.8888 (tpp) REVERT: C 429 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8427 (mm-30) REVERT: D 74 ASP cc_start: 0.9255 (m-30) cc_final: 0.9004 (m-30) REVERT: D 147 MET cc_start: 0.9538 (tpp) cc_final: 0.9115 (mmm) REVERT: D 163 ILE cc_start: 0.9071 (tp) cc_final: 0.8809 (tp) REVERT: D 180 VAL cc_start: 0.9425 (m) cc_final: 0.9139 (p) REVERT: D 257 MET cc_start: 0.8958 (mmm) cc_final: 0.8214 (mmt) REVERT: D 288 GLU cc_start: 0.8913 (tp30) cc_final: 0.8624 (pt0) REVERT: D 330 MET cc_start: 0.9035 (mmp) cc_final: 0.8820 (mmm) REVERT: A 130 GLU cc_start: 0.9455 (mm-30) cc_final: 0.9105 (mm-30) REVERT: A 134 ASP cc_start: 0.9038 (m-30) cc_final: 0.8530 (p0) REVERT: A 177 TYR cc_start: 0.8408 (t80) cc_final: 0.8093 (t80) outliers start: 19 outliers final: 14 residues processed: 186 average time/residue: 0.0781 time to fit residues: 21.3012 Evaluate side-chains 184 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 50 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 73 optimal weight: 0.0030 chunk 125 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.100792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.072849 restraints weight = 37381.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.074764 restraints weight = 18208.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.076084 restraints weight = 11244.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.077026 restraints weight = 8055.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.077628 restraints weight = 6319.640| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10341 Z= 0.252 Angle : 0.767 13.176 14079 Z= 0.389 Chirality : 0.046 0.320 1588 Planarity : 0.004 0.045 1846 Dihedral : 8.805 154.404 1571 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.90 % Favored : 96.02 % Rotamer: Outliers : 1.85 % Allowed : 24.38 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 1.23 (0.24), residues: 1333 helix: 1.84 (0.19), residues: 755 sheet: -0.25 (0.46), residues: 122 loop : -0.58 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 380 TYR 0.034 0.002 TYR C 210 PHE 0.014 0.002 PHE D 167 TRP 0.056 0.003 TRP D 21 HIS 0.011 0.002 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00552 (10340) covalent geometry : angle 0.76711 (14079) hydrogen bonds : bond 0.04254 ( 608) hydrogen bonds : angle 4.43768 ( 1779) Misc. bond : bond 0.00489 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 MET cc_start: 0.9543 (tmm) cc_final: 0.9226 (tmm) REVERT: C 116 ASP cc_start: 0.8912 (p0) cc_final: 0.8593 (p0) REVERT: C 120 ASP cc_start: 0.8737 (m-30) cc_final: 0.8077 (m-30) REVERT: C 377 MET cc_start: 0.8349 (tmm) cc_final: 0.7923 (tmm) REVERT: C 413 MET cc_start: 0.8401 (tpp) cc_final: 0.7611 (tpp) REVERT: C 417 GLU cc_start: 0.8713 (tt0) cc_final: 0.8337 (tt0) REVERT: C 425 MET cc_start: 0.9284 (mmm) cc_final: 0.8745 (tpp) REVERT: C 429 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8508 (mm-30) REVERT: D 74 ASP cc_start: 0.9291 (m-30) cc_final: 0.9034 (m-30) REVERT: D 181 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8191 (mt-10) REVERT: D 186 THR cc_start: 0.9377 (m) cc_final: 0.9061 (p) REVERT: D 257 MET cc_start: 0.8923 (mmm) cc_final: 0.8348 (mmt) REVERT: D 288 GLU cc_start: 0.9016 (tp30) cc_final: 0.8615 (pt0) REVERT: D 363 MET cc_start: 0.8662 (tpp) cc_final: 0.8231 (tpp) REVERT: D 408 PHE cc_start: 0.9483 (m-80) cc_final: 0.9264 (m-80) REVERT: A 136 LEU cc_start: 0.8758 (tp) cc_final: 0.8461 (tp) REVERT: A 177 TYR cc_start: 0.8371 (t80) cc_final: 0.7898 (t80) outliers start: 18 outliers final: 15 residues processed: 172 average time/residue: 0.0769 time to fit residues: 19.8207 Evaluate side-chains 168 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 50 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 23 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 117 optimal weight: 30.0000 chunk 103 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 0.0270 chunk 94 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN B 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.103314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.075146 restraints weight = 36042.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.077148 restraints weight = 17272.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.078573 restraints weight = 10694.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.079377 restraints weight = 7609.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.080050 restraints weight = 6085.980| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10341 Z= 0.137 Angle : 0.713 11.775 14079 Z= 0.360 Chirality : 0.044 0.346 1588 Planarity : 0.004 0.046 1846 Dihedral : 8.561 150.237 1571 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.15 % Favored : 96.77 % Rotamer: Outliers : 1.34 % Allowed : 25.21 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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 aren not related in a simple way. whole: 1.38 (0.24), residues: 1333 helix: 1.93 (0.19), residues: 752 sheet: 0.02 (0.47), residues: 116 loop : -0.50 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 123 TYR 0.023 0.002 TYR B 40 PHE 0.009 0.001 PHE A 198 TRP 0.050 0.003 TRP D 21 HIS 0.005 0.001 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00306 (10340) covalent geometry : angle 0.71322 (14079) hydrogen bonds : bond 0.03862 ( 608) hydrogen bonds : angle 4.25952 ( 1779) Misc. bond : bond 0.00493 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 MET cc_start: 0.9526 (tmm) cc_final: 0.9143 (tmm) REVERT: C 116 ASP cc_start: 0.8867 (p0) cc_final: 0.8512 (p0) REVERT: C 120 ASP cc_start: 0.8672 (m-30) cc_final: 0.7960 (m-30) REVERT: C 141 PHE cc_start: 0.9072 (m-80) cc_final: 0.8777 (m-10) REVERT: C 377 MET cc_start: 0.8367 (tmm) cc_final: 0.7893 (tmm) REVERT: C 413 MET cc_start: 0.8309 (tpp) cc_final: 0.7921 (tpp) REVERT: C 425 MET cc_start: 0.9291 (mmm) cc_final: 0.8790 (tpp) REVERT: C 429 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8265 (mm-30) REVERT: D 74 ASP cc_start: 0.9267 (m-30) cc_final: 0.8995 (m-30) REVERT: D 147 MET cc_start: 0.9529 (tpp) cc_final: 0.9072 (mmm) REVERT: D 180 VAL cc_start: 0.9410 (m) cc_final: 0.9125 (p) REVERT: D 257 MET cc_start: 0.8984 (mmm) cc_final: 0.8329 (mmt) REVERT: D 288 GLU cc_start: 0.8877 (tp30) cc_final: 0.8590 (pt0) REVERT: D 408 PHE cc_start: 0.9434 (m-80) cc_final: 0.9213 (m-80) REVERT: A 130 GLU cc_start: 0.9448 (mm-30) cc_final: 0.9093 (mm-30) REVERT: A 134 ASP cc_start: 0.9065 (m-30) cc_final: 0.8539 (p0) REVERT: A 136 LEU cc_start: 0.8728 (tp) cc_final: 0.8469 (tp) REVERT: A 177 TYR cc_start: 0.8385 (t80) cc_final: 0.7996 (t80) outliers start: 13 outliers final: 9 residues processed: 178 average time/residue: 0.0825 time to fit residues: 21.5924 Evaluate side-chains 173 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 50 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 57 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 104 optimal weight: 40.0000 chunk 85 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.099863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.070858 restraints weight = 38826.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.072726 restraints weight = 19207.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.074051 restraints weight = 12225.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.074968 restraints weight = 8959.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.075433 restraints weight = 7220.818| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 10341 Z= 0.349 Angle : 0.853 12.284 14079 Z= 0.435 Chirality : 0.049 0.320 1588 Planarity : 0.005 0.053 1846 Dihedral : 9.274 160.157 1571 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.43 % Favored : 95.50 % Rotamer: Outliers : 1.54 % Allowed : 25.51 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 0.98 (0.23), residues: 1333 helix: 1.68 (0.19), residues: 755 sheet: -0.30 (0.45), residues: 123 loop : -0.79 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 62 TYR 0.033 0.003 TYR C 224 PHE 0.017 0.002 PHE D 167 TRP 0.072 0.004 TRP D 21 HIS 0.015 0.003 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.00754 (10340) covalent geometry : angle 0.85261 (14079) hydrogen bonds : bond 0.04526 ( 608) hydrogen bonds : angle 4.70601 ( 1779) Misc. bond : bond 0.00551 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1854.71 seconds wall clock time: 32 minutes 45.96 seconds (1965.96 seconds total)