Starting phenix.real_space_refine on Thu May 1 02:48:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qau_18304/05_2025/8qau_18304.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qau_18304/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qau_18304/05_2025/8qau_18304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qau_18304/05_2025/8qau_18304.map" model { file = "/net/cci-nas-00/data/ceres_data/8qau_18304/05_2025/8qau_18304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qau_18304/05_2025/8qau_18304.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 11, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 4} 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: {'GLN:plan1': 11, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 3} 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, 'ASN:plan1': 2, 'HIS:plan': 1} 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: 6.97, per 1000 atoms: 0.69 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: 2.98 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.07 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: 2.95 Time building geometry restraints manager: 3.37 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.090 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.160 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (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 TRP 0.021 0.002 TRP C 388 HIS 0.004 0.001 HIS C 88 PHE 0.019 0.001 PHE C 49 TYR 0.014 0.001 TYR C 282 ARG 0.011 0.000 ARG D 306 Details of bonding type rmsd hydrogen bonds : bond 0.14611 ( 608) hydrogen bonds : angle 6.00362 ( 1779) covalent geometry : bond 0.00402 (10340) covalent geometry : angle 0.69037 (14079) 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 : 1.229 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: 0.5088 (mmm) REVERT: C 346 TRP cc_start: 0.6579 (p-90) cc_final: 0.4146 (t60) REVERT: C 352 LYS cc_start: 0.5687 (mmpt) cc_final: 0.5248 (mmtm) REVERT: A 225 MET cc_start: 0.8826 (mmp) cc_final: 0.8580 (mmm) 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: 0.2270 time to fit residues: 90.9382 Evaluate side-chains 178 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.0980 chunk 53 optimal weight: 5.9990 chunk 103 optimal weight: 30.0000 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 119 optimal weight: 20.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS D 190 HIS ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 HIS D 414 ASN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.106561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.077038 restraints weight = 35952.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.079100 restraints weight = 17200.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.080504 restraints weight = 10509.645| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10341 Z= 0.162 Angle : 0.682 8.150 14079 Z= 0.343 Chirality : 0.043 0.194 1588 Planarity : 0.004 0.042 1846 Dihedral : 15.217 142.303 1571 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 1.95 % Allowed : 13.37 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.23), residues: 1333 helix: 1.62 (0.19), residues: 752 sheet: -0.57 (0.48), residues: 111 loop : -0.75 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 21 HIS 0.006 0.001 HIS C 88 PHE 0.019 0.002 PHE B 97 TYR 0.029 0.002 TYR B 112 ARG 0.006 0.001 ARG D 306 Details of bonding type rmsd hydrogen bonds : bond 0.04568 ( 608) hydrogen bonds : angle 4.56467 ( 1779) covalent geometry : bond 0.00357 (10340) covalent geometry : angle 0.68175 (14079) Misc. bond : bond 0.00157 ( 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 213 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 1.124 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: 0.9433 (tmm) cc_final: 0.9034 (tmm) REVERT: C 141 PHE cc_start: 0.9098 (m-10) cc_final: 0.8763 (m-10) REVERT: C 185 TYR cc_start: 0.9531 (m-80) cc_final: 0.9320 (m-80) REVERT: C 346 TRP cc_start: 0.8719 (p-90) cc_final: 0.4682 (t60) REVERT: C 358 GLU cc_start: 0.9292 (OUTLIER) cc_final: 0.9058 (tp30) REVERT: D 1 MET cc_start: 0.8420 (mmm) cc_final: 0.8210 (mmm) REVERT: D 180 VAL cc_start: 0.9282 (m) cc_final: 0.9058 (p) REVERT: D 181 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7791 (mt-10) REVERT: D 257 MET cc_start: 0.8805 (mmm) cc_final: 0.7908 (mmt) REVERT: D 265 PHE cc_start: 0.9527 (m-80) cc_final: 0.9290 (m-10) REVERT: D 376 GLU cc_start: 0.9410 (mm-30) cc_final: 0.8933 (mm-30) REVERT: D 379 LYS cc_start: 0.8894 (ptpt) cc_final: 0.8399 (ptpt) REVERT: A 177 TYR cc_start: 0.8090 (t80) cc_final: 0.7626 (t80) REVERT: A 225 MET cc_start: 0.8703 (mmp) cc_final: 0.8144 (mtp) outliers start: 19 outliers final: 11 residues processed: 208 average time/residue: 0.1948 time to fit residues: 58.7346 Evaluate side-chains 186 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 189 LEU 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 65 LEU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.9980 chunk 60 optimal weight: 0.1980 chunk 106 optimal weight: 50.0000 chunk 105 optimal weight: 30.0000 chunk 94 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 124 optimal weight: 20.0000 chunk 80 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 65 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 ASN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.107695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.078136 restraints weight = 36344.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.080275 restraints weight = 17470.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.081667 restraints weight = 10601.035| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10341 Z= 0.127 Angle : 0.626 10.444 14079 Z= 0.311 Chirality : 0.042 0.246 1588 Planarity : 0.004 0.042 1846 Dihedral : 13.255 138.104 1571 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.63 % Favored : 97.30 % Rotamer: Outliers : 1.75 % Allowed : 15.74 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.23), residues: 1333 helix: 1.79 (0.19), residues: 755 sheet: -0.51 (0.48), residues: 111 loop : -0.63 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 21 HIS 0.005 0.001 HIS C 88 PHE 0.010 0.001 PHE C 267 TYR 0.019 0.001 TYR C 172 ARG 0.004 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03961 ( 608) hydrogen bonds : angle 4.28131 ( 1779) covalent geometry : bond 0.00270 (10340) covalent geometry : angle 0.62555 (14079) Misc. bond : bond 0.00059 ( 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 212 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 1.144 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: 0.9471 (tmm) cc_final: 0.9000 (tmm) REVERT: C 77 GLU cc_start: 0.8831 (tp30) cc_final: 0.8603 (tp30) REVERT: C 141 PHE cc_start: 0.9047 (m-10) cc_final: 0.8715 (m-10) REVERT: C 221 ARG cc_start: 0.7567 (mmm-85) cc_final: 0.7337 (mmm160) REVERT: C 302 MET cc_start: 0.8398 (mmm) cc_final: 0.7956 (mmt) REVERT: C 346 TRP cc_start: 0.8638 (p-90) cc_final: 0.4830 (t-100) REVERT: C 377 MET cc_start: 0.8321 (tmm) cc_final: 0.7787 (tmm) REVERT: C 413 MET cc_start: 0.8602 (tpp) cc_final: 0.7980 (tpp) REVERT: C 417 GLU cc_start: 0.8532 (tt0) cc_final: 0.8278 (tt0) REVERT: D 1 MET cc_start: 0.8384 (mmm) cc_final: 0.8084 (mmm) REVERT: D 74 ASP cc_start: 0.9234 (m-30) cc_final: 0.8952 (m-30) REVERT: D 180 VAL cc_start: 0.9306 (m) cc_final: 0.9077 (p) REVERT: D 181 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7735 (mt-10) REVERT: A 177 TYR cc_start: 0.8303 (t80) cc_final: 0.7911 (t80) outliers start: 17 outliers final: 7 residues processed: 206 average time/residue: 0.1973 time to fit residues: 59.4746 Evaluate side-chains 182 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 175 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 LEU 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 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 83 optimal weight: 7.9990 chunk 85 optimal weight: 0.0470 chunk 106 optimal weight: 50.0000 chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 309 HIS D 190 HIS ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.106863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.077433 restraints weight = 36223.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.079529 restraints weight = 17573.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.080933 restraints weight = 10761.211| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3267 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= 0.126 Angle : 0.607 7.566 14079 Z= 0.305 Chirality : 0.043 0.464 1588 Planarity : 0.004 0.042 1846 Dihedral : 9.244 138.123 1571 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.93 % Favored : 97.00 % Rotamer: Outliers : 2.16 % Allowed : 17.28 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.23), residues: 1333 helix: 1.97 (0.19), residues: 758 sheet: -0.53 (0.46), residues: 116 loop : -0.60 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 21 HIS 0.004 0.001 HIS C 88 PHE 0.018 0.001 PHE A 153 TYR 0.023 0.001 TYR C 172 ARG 0.003 0.000 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 608) hydrogen bonds : angle 4.13521 ( 1779) covalent geometry : bond 0.00275 (10340) covalent geometry : angle 0.60709 (14079) Misc. bond : bond 0.00080 ( 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 213 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 1.157 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: 0.9513 (tmm) cc_final: 0.9087 (tmm) REVERT: C 69 ASP cc_start: 0.8211 (t0) cc_final: 0.7521 (t70) REVERT: C 141 PHE cc_start: 0.8924 (m-10) cc_final: 0.8629 (m-10) REVERT: C 346 TRP cc_start: 0.8752 (p-90) cc_final: 0.4838 (t-100) REVERT: C 377 MET cc_start: 0.8404 (tmm) cc_final: 0.7825 (tmm) REVERT: C 413 MET cc_start: 0.8548 (tpp) cc_final: 0.8019 (tpp) REVERT: C 417 GLU cc_start: 0.8665 (tt0) cc_final: 0.8455 (tt0) REVERT: D 1 MET cc_start: 0.8427 (mmm) cc_final: 0.8113 (mmm) REVERT: D 74 ASP cc_start: 0.9290 (m-30) cc_final: 0.9020 (m-30) REVERT: D 147 MET cc_start: 0.9558 (tpp) cc_final: 0.9160 (mmm) REVERT: D 180 VAL cc_start: 0.9359 (m) cc_final: 0.9052 (p) REVERT: D 181 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7818 (mt-10) REVERT: D 257 MET cc_start: 0.8939 (mmm) cc_final: 0.8093 (mmt) REVERT: D 312 THR cc_start: 0.7861 (p) cc_final: 0.7141 (p) REVERT: D 375 GLN cc_start: 0.9411 (pm20) cc_final: 0.9204 (pm20) REVERT: D 376 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8968 (mm-30) REVERT: D 379 LYS cc_start: 0.8820 (ptpt) cc_final: 0.8267 (ptpt) REVERT: D 407 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8899 (mp0) REVERT: A 177 TYR cc_start: 0.8355 (t80) cc_final: 0.8051 (t80) REVERT: A 185 ASN cc_start: 0.9513 (m-40) cc_final: 0.9023 (p0) outliers start: 21 outliers final: 11 residues processed: 205 average time/residue: 0.2663 time to fit residues: 78.1250 Evaluate side-chains 186 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 191 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 250 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 A residue 232 LEU 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 94 optimal weight: 0.5980 chunk 103 optimal weight: 20.0000 chunk 51 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.104069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.075137 restraints weight = 36846.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.077228 restraints weight = 17933.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.078589 restraints weight = 11009.952| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10341 Z= 0.169 Angle : 0.630 7.774 14079 Z= 0.320 Chirality : 0.043 0.261 1588 Planarity : 0.004 0.042 1846 Dihedral : 8.817 141.873 1571 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.15 % Favored : 96.77 % Rotamer: Outliers : 2.67 % Allowed : 18.31 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.24), residues: 1333 helix: 2.05 (0.19), residues: 758 sheet: -0.45 (0.46), residues: 116 loop : -0.48 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 21 HIS 0.004 0.001 HIS C 139 PHE 0.016 0.001 PHE D 167 TYR 0.031 0.002 TYR C 210 ARG 0.005 0.001 ARG B 118 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 608) hydrogen bonds : angle 4.09782 ( 1779) covalent geometry : bond 0.00371 (10340) covalent geometry : angle 0.62953 (14079) Misc. bond : bond 0.00199 ( 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 201 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 1.271 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: symmetry clash REVERT: C 36 MET cc_start: 0.9509 (tmm) cc_final: 0.9078 (tmm) REVERT: C 116 ASP cc_start: 0.9003 (p0) cc_final: 0.8645 (p0) REVERT: C 120 ASP cc_start: 0.8749 (m-30) cc_final: 0.8063 (m-30) REVERT: C 141 PHE cc_start: 0.8922 (m-10) cc_final: 0.8618 (m-10) REVERT: C 377 MET cc_start: 0.8396 (tmm) cc_final: 0.8067 (tmm) REVERT: C 413 MET cc_start: 0.8525 (tpp) cc_final: 0.7965 (tpp) REVERT: C 417 GLU cc_start: 0.8738 (tt0) cc_final: 0.8472 (tt0) REVERT: D 1 MET cc_start: 0.8414 (mmm) cc_final: 0.8151 (mmm) REVERT: D 74 ASP cc_start: 0.9246 (m-30) cc_final: 0.9004 (m-30) REVERT: D 180 VAL cc_start: 0.9402 (m) cc_final: 0.9085 (p) REVERT: D 181 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7930 (mt-10) REVERT: D 233 MET cc_start: 0.9056 (mtt) cc_final: 0.8766 (tpp) REVERT: D 257 MET cc_start: 0.8901 (mmm) cc_final: 0.7990 (mmt) REVERT: D 312 THR cc_start: 0.8020 (p) cc_final: 0.7154 (p) REVERT: D 321 MET cc_start: 0.9628 (pmm) cc_final: 0.9389 (pmm) REVERT: D 375 GLN cc_start: 0.9421 (pm20) cc_final: 0.9174 (pm20) REVERT: D 376 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8919 (mm-30) REVERT: D 379 LYS cc_start: 0.8799 (ptpt) cc_final: 0.8290 (ptpt) REVERT: D 407 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8909 (mp0) REVERT: A 177 TYR cc_start: 0.8326 (t80) cc_final: 0.7962 (t80) REVERT: B 58 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8541 (mp0) outliers start: 26 outliers final: 14 residues processed: 193 average time/residue: 0.2703 time to fit residues: 75.9238 Evaluate side-chains 179 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 LEU 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 188 SER Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 374 ILE 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 10 optimal weight: 0.0980 chunk 13 optimal weight: 3.9990 chunk 85 optimal weight: 0.0370 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 73 optimal weight: 0.5980 chunk 37 optimal weight: 0.2980 chunk 116 optimal weight: 30.0000 chunk 33 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 overall best weight: 0.2658 ------------------------------------------------------------------------------- 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** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN B 86 ASN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.106805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.077215 restraints weight = 36753.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.079320 restraints weight = 17725.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.080761 restraints weight = 10845.576| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3874 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= 0.118 Angle : 0.626 10.722 14079 Z= 0.315 Chirality : 0.043 0.302 1588 Planarity : 0.004 0.041 1846 Dihedral : 8.658 137.171 1571 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.55 % Favored : 97.37 % Rotamer: Outliers : 1.85 % Allowed : 20.47 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.23), residues: 1333 helix: 2.00 (0.19), residues: 760 sheet: -0.33 (0.45), residues: 119 loop : -0.44 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 21 HIS 0.007 0.001 HIS C 88 PHE 0.026 0.001 PHE A 153 TYR 0.020 0.001 TYR B 40 ARG 0.004 0.000 ARG C 123 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 608) hydrogen bonds : angle 4.03501 ( 1779) covalent geometry : bond 0.00254 (10340) covalent geometry : angle 0.62611 (14079) Misc. bond : bond 0.00311 ( 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 212 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 1.290 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: 0.9553 (tmm) cc_final: 0.9045 (tmm) REVERT: C 69 ASP cc_start: 0.8110 (t0) cc_final: 0.7903 (t0) REVERT: C 141 PHE cc_start: 0.8848 (m-10) cc_final: 0.8605 (m-10) REVERT: C 154 MET cc_start: 0.9151 (tpp) cc_final: 0.8867 (mmm) REVERT: C 221 ARG cc_start: 0.8046 (mmp80) cc_final: 0.7727 (mmp80) REVERT: C 377 MET cc_start: 0.8411 (tmm) cc_final: 0.7734 (tmm) REVERT: C 388 TRP cc_start: 0.9194 (m100) cc_final: 0.8978 (m100) REVERT: C 413 MET cc_start: 0.8440 (tpp) cc_final: 0.7885 (tpp) REVERT: C 417 GLU cc_start: 0.8698 (tt0) cc_final: 0.8459 (tt0) REVERT: D 1 MET cc_start: 0.8378 (mmm) cc_final: 0.8144 (mmm) REVERT: D 74 ASP cc_start: 0.9212 (m-30) cc_final: 0.8931 (m-30) REVERT: D 147 MET cc_start: 0.9531 (tpp) cc_final: 0.9173 (mmm) REVERT: D 164 MET cc_start: 0.8927 (tpp) cc_final: 0.8694 (tpp) REVERT: D 180 VAL cc_start: 0.9309 (m) cc_final: 0.8952 (p) REVERT: D 233 MET cc_start: 0.9044 (mtt) cc_final: 0.8817 (tpp) REVERT: D 257 MET cc_start: 0.8906 (mmm) cc_final: 0.7946 (mmt) REVERT: D 312 THR cc_start: 0.7517 (p) cc_final: 0.6650 (p) REVERT: D 321 MET cc_start: 0.9674 (pmm) cc_final: 0.9395 (pmm) REVERT: D 375 GLN cc_start: 0.9331 (pm20) cc_final: 0.9020 (pm20) REVERT: D 376 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8934 (mm-30) REVERT: D 379 LYS cc_start: 0.8868 (ptpt) cc_final: 0.8348 (ptpt) REVERT: D 407 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8911 (mt-10) REVERT: A 177 TYR cc_start: 0.8440 (t80) cc_final: 0.8151 (t80) REVERT: B 58 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8490 (mp0) outliers start: 18 outliers final: 9 residues processed: 205 average time/residue: 0.2404 time to fit residues: 70.5601 Evaluate side-chains 181 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 432 TYR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain A residue 198 PHE 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 30 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 85 optimal weight: 0.0020 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.3980 overall best weight: 1.0392 ------------------------------------------------------------------------------- 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** ** B 120 GLN ** 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 = 0.4053 r_free = 0.4053 target = 0.105782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.076733 restraints weight = 36943.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.078861 restraints weight = 17893.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.080236 restraints weight = 10924.437| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10341 Z= 0.132 Angle : 0.666 14.534 14079 Z= 0.331 Chirality : 0.045 0.347 1588 Planarity : 0.004 0.044 1846 Dihedral : 8.284 138.280 1571 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.78 % Favored : 97.15 % Rotamer: Outliers : 1.54 % Allowed : 22.84 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.24), residues: 1333 helix: 2.08 (0.19), residues: 756 sheet: -0.14 (0.45), residues: 119 loop : -0.38 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 21 HIS 0.003 0.001 HIS A 223 PHE 0.011 0.001 PHE D 167 TYR 0.022 0.001 TYR B 40 ARG 0.007 0.000 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 608) hydrogen bonds : angle 4.02200 ( 1779) covalent geometry : bond 0.00293 (10340) covalent geometry : angle 0.66563 (14079) Misc. bond : bond 0.00574 ( 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 190 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 1.183 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: symmetry clash REVERT: C 36 MET cc_start: 0.9548 (tmm) cc_final: 0.9044 (tmm) REVERT: C 69 ASP cc_start: 0.8110 (t0) cc_final: 0.7460 (t70) REVERT: C 121 ARG cc_start: 0.8359 (tpt170) cc_final: 0.7151 (tpt170) REVERT: C 154 MET cc_start: 0.9087 (tpp) cc_final: 0.8811 (mmm) REVERT: C 221 ARG cc_start: 0.8097 (mmp80) cc_final: 0.7589 (mmp80) REVERT: C 377 MET cc_start: 0.8397 (tmm) cc_final: 0.7922 (tmm) REVERT: C 413 MET cc_start: 0.8416 (tpp) cc_final: 0.7913 (tpp) REVERT: C 417 GLU cc_start: 0.8727 (tt0) cc_final: 0.8482 (tt0) REVERT: D 1 MET cc_start: 0.8339 (mmm) cc_final: 0.8112 (mmm) REVERT: D 74 ASP cc_start: 0.9189 (m-30) cc_final: 0.8909 (m-30) REVERT: D 147 MET cc_start: 0.9514 (tpp) cc_final: 0.9167 (mmm) REVERT: D 257 MET cc_start: 0.8855 (mmm) cc_final: 0.8003 (mmt) REVERT: D 312 THR cc_start: 0.7836 (p) cc_final: 0.7116 (p) REVERT: D 375 GLN cc_start: 0.9303 (pm20) cc_final: 0.9019 (pm20) REVERT: D 376 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8906 (mm-30) REVERT: D 379 LYS cc_start: 0.8868 (ptpt) cc_final: 0.8362 (ptpt) REVERT: D 407 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8885 (mt-10) REVERT: A 134 ASP cc_start: 0.9114 (m-30) cc_final: 0.8660 (p0) REVERT: A 136 LEU cc_start: 0.8670 (tp) cc_final: 0.8385 (tp) REVERT: A 177 TYR cc_start: 0.8451 (t80) cc_final: 0.8240 (t80) REVERT: B 53 MET cc_start: 0.3765 (ppp) cc_final: 0.3272 (ppp) outliers start: 15 outliers final: 12 residues processed: 187 average time/residue: 0.2145 time to fit residues: 57.8849 Evaluate side-chains 179 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 269 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 192 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 374 ILE 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 78 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 60 optimal weight: 0.0470 chunk 77 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 16 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 109 optimal weight: 20.0000 chunk 84 optimal weight: 0.8980 overall best weight: 0.7680 ------------------------------------------------------------------------------- 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** ** B 120 GLN ** 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 = 0.4061 r_free = 0.4061 target = 0.106188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.076929 restraints weight = 36980.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.079040 restraints weight = 17841.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.080474 restraints weight = 10917.722| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4199 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= 0.124 Angle : 0.647 11.333 14079 Z= 0.327 Chirality : 0.044 0.328 1588 Planarity : 0.004 0.046 1846 Dihedral : 7.965 137.091 1571 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.63 % Favored : 97.30 % Rotamer: Outliers : 1.75 % Allowed : 22.53 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.24), residues: 1333 helix: 2.09 (0.19), residues: 757 sheet: 0.05 (0.47), residues: 117 loop : -0.35 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 21 HIS 0.004 0.001 HIS A 223 PHE 0.027 0.001 PHE A 153 TYR 0.023 0.001 TYR B 40 ARG 0.007 0.000 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 608) hydrogen bonds : angle 3.99605 ( 1779) covalent geometry : bond 0.00275 (10340) covalent geometry : angle 0.64673 (14079) Misc. bond : bond 0.00601 ( 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 194 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 1.164 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: 0.9550 (tmm) cc_final: 0.9035 (tmm) REVERT: C 141 PHE cc_start: 0.8958 (m-10) cc_final: 0.8647 (m-10) REVERT: C 377 MET cc_start: 0.8398 (tmm) cc_final: 0.7923 (tmm) REVERT: C 388 TRP cc_start: 0.9110 (m100) cc_final: 0.8864 (m100) REVERT: C 413 MET cc_start: 0.8366 (tpp) cc_final: 0.7895 (tpp) REVERT: C 417 GLU cc_start: 0.8705 (tt0) cc_final: 0.8471 (tt0) REVERT: D 1 MET cc_start: 0.8321 (mmm) cc_final: 0.8023 (mmm) REVERT: D 74 ASP cc_start: 0.9180 (m-30) cc_final: 0.8913 (m-30) REVERT: D 147 MET cc_start: 0.9512 (tpp) cc_final: 0.9176 (mmm) REVERT: D 233 MET cc_start: 0.9027 (mtt) cc_final: 0.8783 (mtt) REVERT: D 257 MET cc_start: 0.8837 (mmm) cc_final: 0.7976 (mmt) REVERT: D 312 THR cc_start: 0.7805 (p) cc_final: 0.7112 (p) REVERT: D 321 MET cc_start: 0.9659 (pmm) cc_final: 0.9292 (pmm) REVERT: D 375 GLN cc_start: 0.9243 (pm20) cc_final: 0.8885 (pm20) REVERT: D 376 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8718 (mm-30) REVERT: D 379 LYS cc_start: 0.8907 (ptpt) cc_final: 0.8330 (ptpt) REVERT: D 407 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8898 (mt-10) REVERT: A 136 LEU cc_start: 0.8609 (tp) cc_final: 0.8408 (tp) REVERT: A 177 TYR cc_start: 0.8383 (t80) cc_final: 0.8175 (t80) REVERT: B 58 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8602 (mp0) outliers start: 17 outliers final: 14 residues processed: 187 average time/residue: 0.2024 time to fit residues: 54.9932 Evaluate side-chains 183 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 353 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 354 CYS Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain A residue 126 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 85 optimal weight: 0.5980 chunk 124 optimal weight: 50.0000 chunk 76 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 126 optimal weight: 30.0000 chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 GLN D 329 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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 = 0.4013 r_free = 0.4013 target = 0.103112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.074059 restraints weight = 37529.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.076070 restraints weight = 18336.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.077412 restraints weight = 11331.727| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10341 Z= 0.179 Angle : 0.705 12.540 14079 Z= 0.354 Chirality : 0.044 0.295 1588 Planarity : 0.004 0.043 1846 Dihedral : 8.086 142.344 1571 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 2.16 % Allowed : 23.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.24), residues: 1333 helix: 2.11 (0.19), residues: 758 sheet: -0.01 (0.48), residues: 114 loop : -0.39 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 21 HIS 0.005 0.001 HIS C 139 PHE 0.017 0.001 PHE D 167 TYR 0.025 0.002 TYR C 210 ARG 0.005 0.001 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 608) hydrogen bonds : angle 4.13728 ( 1779) covalent geometry : bond 0.00396 (10340) covalent geometry : angle 0.70468 (14079) Misc. bond : bond 0.00385 ( 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 187 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 1.110 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: 0.9574 (tmm) cc_final: 0.9184 (tmm) REVERT: C 116 ASP cc_start: 0.8987 (p0) cc_final: 0.8613 (p0) REVERT: C 120 ASP cc_start: 0.8739 (m-30) cc_final: 0.8041 (m-30) REVERT: C 377 MET cc_start: 0.8372 (tmm) cc_final: 0.7953 (tmm) REVERT: C 413 MET cc_start: 0.8399 (tpp) cc_final: 0.7832 (tpp) REVERT: C 417 GLU cc_start: 0.8784 (tt0) cc_final: 0.8528 (tt0) REVERT: D 74 ASP cc_start: 0.9168 (m-30) cc_final: 0.8877 (m-30) REVERT: D 147 MET cc_start: 0.9566 (tpp) cc_final: 0.9129 (mmm) REVERT: D 257 MET cc_start: 0.8803 (mmm) cc_final: 0.7893 (mmt) REVERT: D 312 THR cc_start: 0.7948 (p) cc_final: 0.7134 (p) REVERT: D 321 MET cc_start: 0.9625 (pmm) cc_final: 0.9217 (pmm) REVERT: D 403 MET cc_start: 0.8524 (tpp) cc_final: 0.8294 (tpp) REVERT: D 407 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8842 (mp0) REVERT: A 134 ASP cc_start: 0.9183 (m-30) cc_final: 0.8714 (p0) REVERT: A 177 TYR cc_start: 0.8443 (t80) cc_final: 0.8206 (t80) REVERT: B 58 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8672 (mp0) outliers start: 21 outliers final: 19 residues processed: 181 average time/residue: 0.2133 time to fit residues: 56.2781 Evaluate side-chains 181 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 316 CYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 353 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 405 VAL Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain D residue 374 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 103 optimal weight: 40.0000 chunk 49 optimal weight: 0.0770 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 0.0010 chunk 1 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 109 optimal weight: 30.0000 chunk 43 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.3948 ------------------------------------------------------------------------------- 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 86 ASN ** 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 = 0.4032 r_free = 0.4032 target = 0.104500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.075439 restraints weight = 37522.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.077435 restraints weight = 18242.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.078919 restraints weight = 11295.883| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4507 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= 0.146 Angle : 0.690 12.759 14079 Z= 0.347 Chirality : 0.044 0.330 1588 Planarity : 0.004 0.045 1846 Dihedral : 8.046 140.530 1571 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.00 % Favored : 96.92 % Rotamer: Outliers : 1.95 % Allowed : 23.46 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.24), residues: 1333 helix: 2.14 (0.19), residues: 754 sheet: 0.31 (0.48), residues: 113 loop : -0.36 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP D 21 HIS 0.004 0.001 HIS A 223 PHE 0.015 0.001 PHE D 167 TYR 0.023 0.001 TYR B 40 ARG 0.005 0.000 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 608) hydrogen bonds : angle 4.09754 ( 1779) covalent geometry : bond 0.00330 (10340) covalent geometry : angle 0.68995 (14079) Misc. bond : bond 0.00430 ( 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 186 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 1.194 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: 0.9579 (tmm) cc_final: 0.9137 (tmm) REVERT: C 69 ASP cc_start: 0.8211 (t0) cc_final: 0.7728 (t0) REVERT: C 116 ASP cc_start: 0.9011 (p0) cc_final: 0.8640 (p0) REVERT: C 120 ASP cc_start: 0.8777 (m-30) cc_final: 0.8065 (m-30) REVERT: C 141 PHE cc_start: 0.8966 (m-80) cc_final: 0.8627 (m-10) REVERT: C 377 MET cc_start: 0.8412 (tmm) cc_final: 0.7988 (tmm) REVERT: C 388 TRP cc_start: 0.9233 (m100) cc_final: 0.8992 (m100) REVERT: C 413 MET cc_start: 0.8360 (tpp) cc_final: 0.7810 (tpp) REVERT: D 74 ASP cc_start: 0.9200 (m-30) cc_final: 0.8925 (m-30) REVERT: D 147 MET cc_start: 0.9548 (tpp) cc_final: 0.9134 (mmm) REVERT: D 233 MET cc_start: 0.9020 (mtt) cc_final: 0.8572 (mmt) REVERT: D 257 MET cc_start: 0.8837 (mmm) cc_final: 0.7950 (mmt) REVERT: D 288 GLU cc_start: 0.8841 (tp30) cc_final: 0.8558 (pt0) REVERT: D 312 THR cc_start: 0.7610 (p) cc_final: 0.6846 (p) REVERT: D 321 MET cc_start: 0.9646 (pmm) cc_final: 0.9248 (pmm) REVERT: D 379 LYS cc_start: 0.9058 (mtmm) cc_final: 0.8661 (ptpp) REVERT: D 407 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8837 (mp0) REVERT: A 134 ASP cc_start: 0.9130 (m-30) cc_final: 0.8667 (p0) REVERT: A 177 TYR cc_start: 0.8502 (t80) cc_final: 0.8228 (t80) REVERT: B 58 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8677 (mp0) outliers start: 19 outliers final: 18 residues processed: 179 average time/residue: 0.2012 time to fit residues: 52.1947 Evaluate side-chains 183 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 316 CYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 353 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 60 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain D residue 374 ILE 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 5 optimal weight: 0.0670 chunk 98 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 107 optimal weight: 20.0000 chunk 103 optimal weight: 40.0000 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.104677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.075231 restraints weight = 37213.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.077361 restraints weight = 18205.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.078737 restraints weight = 11199.368| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10341 Z= 0.149 Angle : 0.691 10.987 14079 Z= 0.348 Chirality : 0.044 0.324 1588 Planarity : 0.004 0.047 1846 Dihedral : 7.938 140.074 1571 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.08 % Favored : 96.85 % Rotamer: Outliers : 2.16 % Allowed : 23.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.24), residues: 1333 helix: 2.10 (0.19), residues: 761 sheet: 0.53 (0.50), residues: 106 loop : -0.43 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP D 21 HIS 0.004 0.001 HIS A 223 PHE 0.015 0.001 PHE D 167 TYR 0.021 0.001 TYR B 40 ARG 0.004 0.000 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 608) hydrogen bonds : angle 4.11868 ( 1779) covalent geometry : bond 0.00337 (10340) covalent geometry : angle 0.69103 (14079) Misc. bond : bond 0.00411 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4173.43 seconds wall clock time: 75 minutes 10.27 seconds (4510.27 seconds total)