Starting phenix.real_space_refine on Fri Jul 3 00:37:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g81_29831/07_2026/8g81_29831.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g81_29831/07_2026/8g81_29831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g81_29831/07_2026/8g81_29831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g81_29831/07_2026/8g81_29831.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g81_29831/07_2026/8g81_29831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g81_29831/07_2026/8g81_29831.map" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.119 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 38 5.16 5 C 7104 2.51 5 N 1920 2.21 5 O 2084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11148 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4180 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 34, 'TRANS': 504} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 4176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4176 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 34, 'TRANS': 504} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 7, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1353 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "D" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1353 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.11, per 1000 atoms: 0.19 Number of scatterers: 11148 At special positions: 0 Unit cell: (87.98, 127.82, 155.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 38 16.00 O 2084 8.00 N 1920 7.00 C 7104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 328 " distance=2.03 Simple disulfide: pdb=" SG CYS B 106 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS B 328 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1017 " - " ASN A 98 " " NAG A1018 " - " ASN A 522 " " NAG B1017 " - " ASN B 98 " " NAG B1018 " - " ASN B 522 " " NAG C1008 " - " ASN C 184 " " NAG D1008 " - " ASN D 184 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 415.6 milliseconds 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2604 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 9 sheets defined 29.3% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 232 through 253 removed outlier: 5.544A pdb=" N ALA A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N HIS A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 275 Processing helix chain 'A' and resid 303 through 316 removed outlier: 4.020A pdb=" N TYR A 307 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 331 removed outlier: 3.545A pdb=" N ARG A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 339 removed outlier: 3.670A pdb=" N LEU A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 removed outlier: 3.553A pdb=" N GLN A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN A 370 " --> pdb=" O ILE A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 418 removed outlier: 3.898A pdb=" N THR A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 removed outlier: 3.562A pdb=" N TYR A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 460 removed outlier: 3.546A pdb=" N ARG A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR A 450 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.611A pdb=" N ALA A 464 " --> pdb=" O TRP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 524 through 545 Processing helix chain 'A' and resid 594 through 604 Processing helix chain 'A' and resid 605 through 608 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 126 through 134 removed outlier: 3.958A pdb=" N TYR B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.741A pdb=" N MET B 195 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE B 196 " --> pdb=" O GLY B 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 192 through 196' Processing helix chain 'B' and resid 199 through 206 Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 232 through 249 Processing helix chain 'B' and resid 265 through 274 removed outlier: 3.579A pdb=" N SER B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 316 removed outlier: 4.020A pdb=" N TYR B 307 " --> pdb=" O GLN B 303 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 310 " --> pdb=" O LYS B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 332 Processing helix chain 'B' and resid 363 through 370 Processing helix chain 'B' and resid 402 through 418 removed outlier: 3.748A pdb=" N PHE B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 removed outlier: 3.640A pdb=" N TYR B 435 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 441 removed outlier: 3.824A pdb=" N ARG B 441 " --> pdb=" O TRP B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 447 through 460 Processing helix chain 'B' and resid 460 through 473 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 524 through 544 Processing helix chain 'B' and resid 594 through 604 Processing helix chain 'B' and resid 605 through 608 Processing helix chain 'C' and resid 268 through 273 Processing helix chain 'D' and resid 267 through 274 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.793A pdb=" N ARG A 50 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 73 removed outlier: 4.999A pdb=" N LEU A 144 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 209 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL A 210 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N MET A 180 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N LEU A 212 " --> pdb=" O MET A 180 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE A 182 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS A 177 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLU A 257 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N VAL A 179 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE A 259 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 181 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE A 261 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU A 183 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY A 263 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LYS A 286 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 259 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ILE A 288 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 261 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N GLN A 290 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLY A 263 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N MET A 378 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N TYR A 481 " --> pdb=" O MET A 378 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE A 380 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N PHE A 483 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL A 382 " --> pdb=" O PHE A 483 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N LEU A 581 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE A 480 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE A 583 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N THR A 482 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 580 " --> pdb=" O ARG A 590 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 45 removed outlier: 6.768A pdb=" N ARG B 50 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.592A pdb=" N VAL B 209 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL B 210 " --> pdb=" O PRO B 178 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N MET B 180 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU B 212 " --> pdb=" O MET B 180 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N PHE B 182 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 10.668A pdb=" N LYS B 177 " --> pdb=" O PRO B 256 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG B 258 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 179 " --> pdb=" O ARG B 258 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS B 286 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE B 259 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ILE B 288 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 261 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLN B 290 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLY B 263 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N MET B 378 " --> pdb=" O TYR B 479 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N TYR B 481 " --> pdb=" O MET B 378 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE B 380 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N PHE B 483 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL B 382 " --> pdb=" O PHE B 483 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N LEU B 581 " --> pdb=" O VAL B 478 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE B 480 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE B 583 " --> pdb=" O PHE B 480 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N THR B 482 " --> pdb=" O ILE B 583 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 158 through 163 removed outlier: 3.913A pdb=" N ILE C 148 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE C 143 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL C 125 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR C 242 " --> pdb=" O ASP C 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 195 through 197 removed outlier: 4.151A pdb=" N GLY C 116 " --> pdb=" O GLY C 260 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLY C 260 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N SER C 118 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU C 258 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N LYS C 91 " --> pdb=" O ARG C 286 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N ARG C 286 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLY C 93 " --> pdb=" O ASN C 284 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 195 through 197 removed outlier: 6.430A pdb=" N ARG D 112 " --> pdb=" O TYR D 263 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR D 263 " --> pdb=" O ARG D 112 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA D 114 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU D 261 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 158 through 162 removed outlier: 3.526A pdb=" N VAL D 127 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE D 143 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL D 125 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR D 242 " --> pdb=" O ASP D 130 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1077 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3169 1.33 - 1.45: 2058 1.45 - 1.57: 6136 1.57 - 1.69: 1 1.69 - 1.82: 62 Bond restraints: 11426 Sorted by residual: bond pdb=" CB PRO A 77 " pdb=" CG PRO A 77 " ideal model delta sigma weight residual 1.492 1.628 -0.136 5.00e-02 4.00e+02 7.44e+00 bond pdb=" N ARG C 232 " pdb=" CA ARG C 232 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.22e-02 6.72e+03 6.47e+00 bond pdb=" N ARG D 232 " pdb=" CA ARG D 232 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.49e+00 bond pdb=" C ARG C 232 " pdb=" O ARG C 232 " ideal model delta sigma weight residual 1.235 1.212 0.023 1.20e-02 6.94e+03 3.53e+00 bond pdb=" NE ARG C 232 " pdb=" CZ ARG C 232 " ideal model delta sigma weight residual 1.326 1.346 -0.020 1.10e-02 8.26e+03 3.33e+00 ... (remaining 11421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 15384 2.37 - 4.73: 159 4.73 - 7.10: 11 7.10 - 9.46: 4 9.46 - 11.83: 3 Bond angle restraints: 15561 Sorted by residual: angle pdb=" CA PRO A 77 " pdb=" N PRO A 77 " pdb=" CD PRO A 77 " ideal model delta sigma weight residual 112.00 102.93 9.07 1.40e+00 5.10e-01 4.20e+01 angle pdb=" CA ARG C 232 " pdb=" C ARG C 232 " pdb=" O ARG C 232 " ideal model delta sigma weight residual 120.81 114.89 5.92 1.15e+00 7.56e-01 2.65e+01 angle pdb=" CB ARG C 232 " pdb=" CG ARG C 232 " pdb=" CD ARG C 232 " ideal model delta sigma weight residual 111.30 121.24 -9.94 2.30e+00 1.89e-01 1.87e+01 angle pdb=" N GLU B 392 " pdb=" CA GLU B 392 " pdb=" C GLU B 392 " ideal model delta sigma weight residual 114.56 109.40 5.16 1.27e+00 6.20e-01 1.65e+01 angle pdb=" CB MET D 271 " pdb=" CG MET D 271 " pdb=" SD MET D 271 " ideal model delta sigma weight residual 112.70 124.53 -11.83 3.00e+00 1.11e-01 1.56e+01 ... (remaining 15556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 6007 17.82 - 35.64: 605 35.64 - 53.46: 135 53.46 - 71.28: 21 71.28 - 89.10: 9 Dihedral angle restraints: 6777 sinusoidal: 2687 harmonic: 4090 Sorted by residual: dihedral pdb=" CB CYS B 317 " pdb=" SG CYS B 317 " pdb=" SG CYS B 328 " pdb=" CB CYS B 328 " ideal model delta sinusoidal sigma weight residual -86.00 -122.05 36.05 1 1.00e+01 1.00e-02 1.84e+01 dihedral pdb=" CA MET A 446 " pdb=" C MET A 446 " pdb=" N ARG A 447 " pdb=" CA ARG A 447 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PHE A 41 " pdb=" C PHE A 41 " pdb=" N PRO A 42 " pdb=" CA PRO A 42 " ideal model delta harmonic sigma weight residual 180.00 -163.36 -16.64 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 6774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1529 0.075 - 0.150: 179 0.150 - 0.226: 3 0.226 - 0.301: 2 0.301 - 0.376: 1 Chirality restraints: 1714 Sorted by residual: chirality pdb=" C1 NAG B1017 " pdb=" ND2 ASN B 98 " pdb=" C2 NAG B1017 " pdb=" O5 NAG B1017 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA ARG C 232 " pdb=" N ARG C 232 " pdb=" C ARG C 232 " pdb=" CB ARG C 232 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C1 NAG B1018 " pdb=" ND2 ASN B 522 " pdb=" C2 NAG B1018 " pdb=" O5 NAG B1018 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1711 not shown) Planarity restraints: 2043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 76 " -0.065 5.00e-02 4.00e+02 9.36e-02 1.40e+01 pdb=" N PRO A 77 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 77 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 77 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 375 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C ASN B 375 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN B 375 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR B 376 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 549 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO B 550 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 550 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 550 " 0.029 5.00e-02 4.00e+02 ... (remaining 2040 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 126 2.63 - 3.20: 9454 3.20 - 3.76: 16797 3.76 - 4.33: 23573 4.33 - 4.90: 40156 Nonbonded interactions: 90106 Sorted by model distance: nonbonded pdb=" OE1 GLN A 370 " pdb=" NH2 ARG C 232 " model vdw 2.059 3.120 nonbonded pdb=" O LYS D 91 " pdb=" ND2 ASN D 284 " model vdw 2.212 3.120 nonbonded pdb=" OG1 THR D 119 " pdb=" O GLN D 255 " model vdw 2.218 3.040 nonbonded pdb=" O ASN B 375 " pdb=" ND2 ASN B 375 " model vdw 2.234 3.120 nonbonded pdb=" O HIS A 471 " pdb=" OG SER A 476 " model vdw 2.257 3.040 ... (remaining 90101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 1018)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.140 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 : 0.003 0.136 11436 Z= 0.137 Angle : 0.597 11.831 15587 Z= 0.306 Chirality : 0.046 0.376 1714 Planarity : 0.004 0.094 2037 Dihedral : 15.083 89.103 4161 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.69 % Allowed : 21.25 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.22), residues: 1416 helix: 0.51 (0.29), residues: 348 sheet: 0.33 (0.32), residues: 300 loop : -1.20 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 346 TYR 0.018 0.001 TYR C 138 PHE 0.020 0.001 PHE A 413 TRP 0.011 0.001 TRP A 122 HIS 0.002 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (11426) covalent geometry : angle 0.58797 / 0.30 (15561) SS BOND : bond 0.00268 / 0.14 ( 4) SS BOND : angle 0.59706 / 0.37 ( 8) hydrogen bonds : bond 0.16283 / 10.43 ( 377) hydrogen bonds : angle 7.25778 / 5.31 ( 1077) link_NAG-ASN : bond 0.00590 / 0.29 ( 6) link_NAG-ASN : angle 3.07171 / 1.83 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.7519 (mmt90) cc_final: 0.7182 (mmt90) REVERT: B 440 ASP cc_start: 0.8206 (t0) cc_final: 0.7958 (t0) REVERT: B 553 GLN cc_start: 0.6518 (OUTLIER) cc_final: 0.6087 (mp-120) REVERT: C 104 ASP cc_start: 0.8319 (t0) cc_final: 0.7435 (t0) REVERT: C 232 ARG cc_start: 0.6296 (OUTLIER) cc_final: 0.5655 (mmm-85) REVERT: D 271 MET cc_start: 0.5511 (ppp) cc_final: 0.4932 (ptp) outliers start: 8 outliers final: 6 residues processed: 137 average time/residue: 0.1009 time to fit residues: 19.8292 Evaluate side-chains 130 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain D residue 232 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN B 109 ASN ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.175729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110032 restraints weight = 12390.840| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.92 r_work: 0.2932 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.0629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11436 Z= 0.176 Angle : 0.590 9.563 15587 Z= 0.296 Chirality : 0.046 0.321 1714 Planarity : 0.004 0.049 2037 Dihedral : 6.564 58.372 1700 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.51 % Allowed : 19.60 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.22), residues: 1416 helix: 0.85 (0.30), residues: 346 sheet: 0.11 (0.31), residues: 298 loop : -1.20 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.013 0.001 TYR B 481 PHE 0.021 0.002 PHE A 413 TRP 0.009 0.001 TRP A 122 HIS 0.003 0.001 HIS B 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (11426) covalent geometry : angle 0.58311 / 0.29 (15561) SS BOND : bond 0.00397 / 0.20 ( 4) SS BOND : angle 0.83010 / 0.49 ( 8) hydrogen bonds : bond 0.03877 / 2.68 ( 377) hydrogen bonds : angle 5.29455 / 3.81 ( 1077) link_NAG-ASN : bond 0.00477 / 0.23 ( 6) link_NAG-ASN : angle 2.76119 / 1.60 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 123 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.6392 (OUTLIER) cc_final: 0.4878 (t80) REVERT: A 55 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.6534 (ttp-110) REVERT: B 109 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8731 (t0) REVERT: B 276 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7651 (mt) REVERT: B 446 MET cc_start: 0.7669 (tmt) cc_final: 0.7333 (tmm) REVERT: B 553 GLN cc_start: 0.6699 (OUTLIER) cc_final: 0.6060 (mp-120) REVERT: C 104 ASP cc_start: 0.8294 (t0) cc_final: 0.7435 (t0) REVERT: C 232 ARG cc_start: 0.6186 (OUTLIER) cc_final: 0.5490 (mtp-110) REVERT: D 232 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.6359 (ttm110) REVERT: D 271 MET cc_start: 0.5798 (ppp) cc_final: 0.5571 (ptp) outliers start: 52 outliers final: 32 residues processed: 155 average time/residue: 0.0898 time to fit residues: 19.7123 Evaluate side-chains 155 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 232 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 80 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 111 optimal weight: 0.0020 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 340 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 = 0.4005 r_free = 0.4005 target = 0.178603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112825 restraints weight = 12505.286| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.96 r_work: 0.2955 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11436 Z= 0.100 Angle : 0.525 9.595 15587 Z= 0.262 Chirality : 0.044 0.279 1714 Planarity : 0.003 0.035 2037 Dihedral : 5.984 56.674 1694 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.42 % Allowed : 20.21 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.22), residues: 1416 helix: 0.99 (0.30), residues: 352 sheet: 0.11 (0.31), residues: 300 loop : -1.12 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 112 TYR 0.011 0.001 TYR B 481 PHE 0.019 0.001 PHE A 413 TRP 0.009 0.001 TRP B 122 HIS 0.003 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (11426) covalent geometry : angle 0.51979 / 0.26 (15561) SS BOND : bond 0.00253 / 0.13 ( 4) SS BOND : angle 0.53396 / 0.27 ( 8) hydrogen bonds : bond 0.03294 / 2.25 ( 377) hydrogen bonds : angle 4.95257 / 3.57 ( 1077) link_NAG-ASN : bond 0.00463 / 0.23 ( 6) link_NAG-ASN : angle 2.30548 / 1.31 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 137 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 41 PHE cc_start: 0.6154 (OUTLIER) cc_final: 0.4614 (t80) REVERT: A 430 THR cc_start: 0.8565 (t) cc_final: 0.8263 (m) REVERT: B 276 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7704 (mt) REVERT: B 300 VAL cc_start: 0.8914 (m) cc_final: 0.8660 (t) REVERT: B 324 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7408 (pt0) REVERT: B 434 MET cc_start: 0.8350 (tpp) cc_final: 0.7994 (tpt) REVERT: B 440 ASP cc_start: 0.7914 (t0) cc_final: 0.7577 (t0) REVERT: B 446 MET cc_start: 0.7570 (tmt) cc_final: 0.7152 (tmm) REVERT: B 585 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6715 (mt) REVERT: C 104 ASP cc_start: 0.8315 (t0) cc_final: 0.7424 (t0) REVERT: C 232 ARG cc_start: 0.6210 (OUTLIER) cc_final: 0.5514 (mtp-110) REVERT: D 232 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6520 (ttm110) outliers start: 51 outliers final: 31 residues processed: 168 average time/residue: 0.0918 time to fit residues: 22.2100 Evaluate side-chains 156 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 232 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 18 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 131 optimal weight: 0.0170 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 375 ASN ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.175345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110075 restraints weight = 12467.508| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.87 r_work: 0.2922 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11436 Z= 0.187 Angle : 0.571 9.759 15587 Z= 0.287 Chirality : 0.046 0.260 1714 Planarity : 0.004 0.036 2037 Dihedral : 5.891 56.101 1693 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 5.20 % Allowed : 21.51 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.22), residues: 1416 helix: 0.97 (0.30), residues: 348 sheet: 0.04 (0.31), residues: 298 loop : -1.15 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 55 TYR 0.017 0.001 TYR C 138 PHE 0.022 0.002 PHE A 413 TRP 0.006 0.001 TRP B 122 HIS 0.005 0.001 HIS B 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (11426) covalent geometry : angle 0.56550 / 0.29 (15561) SS BOND : bond 0.00385 / 0.20 ( 4) SS BOND : angle 0.82429 / 0.44 ( 8) hydrogen bonds : bond 0.03487 / 2.42 ( 377) hydrogen bonds : angle 4.93157 / 3.54 ( 1077) link_NAG-ASN : bond 0.00411 / 0.20 ( 6) link_NAG-ASN : angle 2.27638 / 1.36 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 118 time to evaluate : 0.301 Fit side-chains REVERT: A 41 PHE cc_start: 0.6406 (OUTLIER) cc_final: 0.4823 (t80) REVERT: B 50 ARG cc_start: 0.6630 (mtm-85) cc_final: 0.6427 (ttp-110) REVERT: B 204 TYR cc_start: 0.8056 (t80) cc_final: 0.7706 (t80) REVERT: B 276 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7709 (mt) REVERT: B 300 VAL cc_start: 0.8939 (m) cc_final: 0.8691 (t) REVERT: B 440 ASP cc_start: 0.8057 (t0) cc_final: 0.7752 (t0) REVERT: B 446 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7137 (tmt) REVERT: B 585 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6717 (mt) REVERT: C 104 ASP cc_start: 0.8372 (t0) cc_final: 0.7454 (t0) REVERT: C 232 ARG cc_start: 0.6259 (OUTLIER) cc_final: 0.5509 (mtp-110) REVERT: D 232 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6591 (ttm110) outliers start: 60 outliers final: 42 residues processed: 159 average time/residue: 0.0893 time to fit residues: 20.5657 Evaluate side-chains 166 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 118 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 232 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 127 optimal weight: 40.0000 chunk 53 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 44 optimal weight: 0.2980 chunk 124 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 11 optimal weight: 0.0370 chunk 80 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 109 ASN B 375 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.178289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.112597 restraints weight = 12402.738| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.95 r_work: 0.2961 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11436 Z= 0.107 Angle : 0.518 9.749 15587 Z= 0.260 Chirality : 0.044 0.257 1714 Planarity : 0.003 0.035 2037 Dihedral : 5.643 55.599 1693 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.86 % Allowed : 21.86 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.22), residues: 1416 helix: 1.09 (0.30), residues: 352 sheet: 0.14 (0.31), residues: 300 loop : -1.06 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 55 TYR 0.011 0.001 TYR B 481 PHE 0.020 0.001 PHE A 413 TRP 0.008 0.001 TRP B 122 HIS 0.002 0.000 HIS B 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (11426) covalent geometry : angle 0.51453 / 0.26 (15561) SS BOND : bond 0.00240 / 0.12 ( 4) SS BOND : angle 0.56155 / 0.28 ( 8) hydrogen bonds : bond 0.03041 / 2.08 ( 377) hydrogen bonds : angle 4.72242 / 3.40 ( 1077) link_NAG-ASN : bond 0.00353 / 0.17 ( 6) link_NAG-ASN : angle 1.94402 / 1.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 134 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 41 PHE cc_start: 0.6158 (OUTLIER) cc_final: 0.4581 (t80) REVERT: A 56 ARG cc_start: 0.7576 (mmt90) cc_final: 0.6965 (mmt90) REVERT: A 430 THR cc_start: 0.8564 (t) cc_final: 0.8261 (m) REVERT: B 50 ARG cc_start: 0.6560 (mtm-85) cc_final: 0.6359 (ttp-110) REVERT: B 109 ASN cc_start: 0.9033 (OUTLIER) cc_final: 0.8741 (t0) REVERT: B 276 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7722 (mt) REVERT: B 300 VAL cc_start: 0.8887 (m) cc_final: 0.8678 (t) REVERT: B 440 ASP cc_start: 0.7975 (t0) cc_final: 0.7632 (t0) REVERT: B 446 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.6932 (tmm) REVERT: B 585 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6713 (mt) REVERT: C 104 ASP cc_start: 0.8350 (t0) cc_final: 0.7474 (t0) REVERT: C 232 ARG cc_start: 0.6247 (OUTLIER) cc_final: 0.5503 (mtp-110) REVERT: D 232 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6027 (ttm110) outliers start: 56 outliers final: 35 residues processed: 170 average time/residue: 0.0837 time to fit residues: 20.5213 Evaluate side-chains 164 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 232 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 100 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 139 optimal weight: 0.0270 chunk 132 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 375 ASN B 500 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.177534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.115678 restraints weight = 12549.325| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.36 r_work: 0.2947 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11436 Z= 0.137 Angle : 0.534 9.753 15587 Z= 0.267 Chirality : 0.045 0.263 1714 Planarity : 0.003 0.035 2037 Dihedral : 5.612 55.472 1693 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 5.20 % Allowed : 21.51 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.22), residues: 1416 helix: 1.09 (0.30), residues: 352 sheet: 0.11 (0.31), residues: 300 loop : -1.06 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 55 TYR 0.016 0.001 TYR C 138 PHE 0.021 0.001 PHE A 413 TRP 0.008 0.001 TRP B 460 HIS 0.004 0.001 HIS B 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (11426) covalent geometry : angle 0.53016 / 0.27 (15561) SS BOND : bond 0.00315 / 0.16 ( 4) SS BOND : angle 0.62810 / 0.33 ( 8) hydrogen bonds : bond 0.03104 / 2.14 ( 377) hydrogen bonds : angle 4.71634 / 3.39 ( 1077) link_NAG-ASN : bond 0.00348 / 0.17 ( 6) link_NAG-ASN : angle 1.91440 / 1.12 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 124 time to evaluate : 0.403 Fit side-chains REVERT: A 41 PHE cc_start: 0.6302 (OUTLIER) cc_final: 0.4719 (t80) REVERT: A 56 ARG cc_start: 0.7618 (mmt90) cc_final: 0.6980 (mmt90) REVERT: B 50 ARG cc_start: 0.6602 (mtm-85) cc_final: 0.6397 (ttp-110) REVERT: B 276 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7760 (mt) REVERT: B 300 VAL cc_start: 0.8913 (m) cc_final: 0.8692 (t) REVERT: B 440 ASP cc_start: 0.7979 (t0) cc_final: 0.7666 (t0) REVERT: B 446 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7029 (tmt) REVERT: B 585 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6739 (mt) REVERT: C 104 ASP cc_start: 0.8387 (t0) cc_final: 0.7470 (t0) REVERT: C 232 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.5484 (mtp85) REVERT: D 271 MET cc_start: 0.5630 (ppp) cc_final: 0.5403 (pmm) outliers start: 60 outliers final: 47 residues processed: 163 average time/residue: 0.0820 time to fit residues: 19.5206 Evaluate side-chains 172 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 120 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 106 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 GLN B 375 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.173906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.107954 restraints weight = 12637.823| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.94 r_work: 0.2895 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 11436 Z= 0.235 Angle : 0.603 9.799 15587 Z= 0.305 Chirality : 0.048 0.264 1714 Planarity : 0.004 0.038 2037 Dihedral : 5.709 55.334 1689 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.46 % Allowed : 21.68 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.22), residues: 1416 helix: 0.89 (0.29), residues: 350 sheet: -0.06 (0.30), residues: 302 loop : -1.16 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 112 TYR 0.016 0.002 TYR A 481 PHE 0.025 0.002 PHE A 413 TRP 0.006 0.001 TRP A 538 HIS 0.006 0.001 HIS B 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.23 (11426) covalent geometry : angle 0.59915 / 0.30 (15561) SS BOND : bond 0.00485 / 0.25 ( 4) SS BOND : angle 0.99099 / 0.55 ( 8) hydrogen bonds : bond 0.03578 / 2.50 ( 377) hydrogen bonds : angle 4.93115 / 3.54 ( 1077) link_NAG-ASN : bond 0.00316 / 0.16 ( 6) link_NAG-ASN : angle 2.12073 / 1.29 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 122 time to evaluate : 0.328 Fit side-chains REVERT: A 41 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.4984 (t80) REVERT: A 497 ASP cc_start: 0.6788 (OUTLIER) cc_final: 0.6345 (t0) REVERT: B 50 ARG cc_start: 0.6633 (mtm-85) cc_final: 0.6412 (ttp-110) REVERT: B 204 TYR cc_start: 0.8087 (t80) cc_final: 0.7749 (t80) REVERT: B 300 VAL cc_start: 0.8947 (m) cc_final: 0.8697 (t) REVERT: B 440 ASP cc_start: 0.8138 (t0) cc_final: 0.7859 (t0) REVERT: B 446 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7103 (tmt) REVERT: B 565 PHE cc_start: 0.7184 (m-80) cc_final: 0.6919 (m-10) REVERT: B 585 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6714 (mt) REVERT: C 153 ASN cc_start: 0.7307 (t0) cc_final: 0.6972 (t0) REVERT: C 232 ARG cc_start: 0.6301 (OUTLIER) cc_final: 0.5596 (mtp-110) REVERT: D 271 MET cc_start: 0.5739 (ppp) cc_final: 0.5513 (ptp) outliers start: 63 outliers final: 51 residues processed: 165 average time/residue: 0.0820 time to fit residues: 19.4943 Evaluate side-chains 175 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 119 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 1 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 109 ASN B 340 GLN B 375 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.177872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112529 restraints weight = 12419.724| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.87 r_work: 0.2947 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11436 Z= 0.110 Angle : 0.524 9.798 15587 Z= 0.264 Chirality : 0.044 0.247 1714 Planarity : 0.003 0.036 2037 Dihedral : 5.414 55.626 1689 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 5.03 % Allowed : 22.46 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.22), residues: 1416 helix: 1.07 (0.30), residues: 350 sheet: 0.07 (0.31), residues: 300 loop : -1.07 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 346 TYR 0.020 0.001 TYR C 138 PHE 0.020 0.001 PHE A 413 TRP 0.009 0.001 TRP B 122 HIS 0.002 0.001 HIS B 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (11426) covalent geometry : angle 0.52043 / 0.26 (15561) SS BOND : bond 0.00245 / 0.13 ( 4) SS BOND : angle 0.60980 / 0.37 ( 8) hydrogen bonds : bond 0.03001 / 2.07 ( 377) hydrogen bonds : angle 4.70994 / 3.39 ( 1077) link_NAG-ASN : bond 0.00341 / 0.17 ( 6) link_NAG-ASN : angle 1.82502 / 1.08 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 136 time to evaluate : 0.395 Fit side-chains REVERT: A 41 PHE cc_start: 0.6256 (OUTLIER) cc_final: 0.4722 (t80) REVERT: A 56 ARG cc_start: 0.7571 (mmt90) cc_final: 0.6980 (mmt90) REVERT: A 497 ASP cc_start: 0.6544 (OUTLIER) cc_final: 0.6138 (t0) REVERT: B 109 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8812 (t0) REVERT: B 300 VAL cc_start: 0.8843 (m) cc_final: 0.8619 (t) REVERT: B 440 ASP cc_start: 0.7960 (t0) cc_final: 0.7608 (t0) REVERT: B 446 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6868 (tmt) REVERT: B 565 PHE cc_start: 0.7145 (m-80) cc_final: 0.6883 (m-10) REVERT: B 585 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6752 (mt) REVERT: C 104 ASP cc_start: 0.8364 (t0) cc_final: 0.7590 (t0) REVERT: C 153 ASN cc_start: 0.7181 (t0) cc_final: 0.6898 (t0) REVERT: C 232 ARG cc_start: 0.6326 (OUTLIER) cc_final: 0.5564 (mtp-110) REVERT: C 271 MET cc_start: 0.8237 (mtm) cc_final: 0.7736 (mtm) outliers start: 58 outliers final: 44 residues processed: 173 average time/residue: 0.0866 time to fit residues: 21.8720 Evaluate side-chains 174 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 124 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 125 optimal weight: 0.3980 chunk 139 optimal weight: 30.0000 chunk 107 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 GLN B 375 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.177132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111761 restraints weight = 12396.236| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.87 r_work: 0.2943 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11436 Z= 0.136 Angle : 0.544 9.802 15587 Z= 0.274 Chirality : 0.045 0.251 1714 Planarity : 0.004 0.035 2037 Dihedral : 5.408 55.539 1689 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 5.29 % Allowed : 22.64 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.22), residues: 1416 helix: 1.12 (0.30), residues: 352 sheet: 0.06 (0.31), residues: 300 loop : -1.07 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 112 TYR 0.017 0.001 TYR C 138 PHE 0.021 0.001 PHE A 413 TRP 0.007 0.001 TRP B 460 HIS 0.003 0.001 HIS B 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (11426) covalent geometry : angle 0.54046 / 0.27 (15561) SS BOND : bond 0.00262 / 0.14 ( 4) SS BOND : angle 0.65768 / 0.40 ( 8) hydrogen bonds : bond 0.03084 / 2.12 ( 377) hydrogen bonds : angle 4.73576 / 3.39 ( 1077) link_NAG-ASN : bond 0.00329 / 0.16 ( 6) link_NAG-ASN : angle 1.97202 / 1.30 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 132 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 41 PHE cc_start: 0.6333 (OUTLIER) cc_final: 0.4772 (t80) REVERT: A 56 ARG cc_start: 0.7589 (mmt90) cc_final: 0.6980 (mmt90) REVERT: A 497 ASP cc_start: 0.6547 (OUTLIER) cc_final: 0.6128 (t0) REVERT: B 50 ARG cc_start: 0.6484 (ttp-110) cc_final: 0.6151 (mtp-110) REVERT: B 143 TYR cc_start: 0.8206 (m-80) cc_final: 0.7657 (m-10) REVERT: B 300 VAL cc_start: 0.8875 (m) cc_final: 0.8637 (t) REVERT: B 440 ASP cc_start: 0.7977 (t0) cc_final: 0.7614 (t0) REVERT: B 446 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6913 (tmt) REVERT: B 565 PHE cc_start: 0.7106 (m-80) cc_final: 0.6859 (m-10) REVERT: B 585 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6730 (mt) REVERT: C 104 ASP cc_start: 0.8375 (t0) cc_final: 0.7589 (t0) REVERT: C 138 TYR cc_start: 0.7774 (p90) cc_final: 0.7574 (p90) REVERT: C 153 ASN cc_start: 0.7195 (t0) cc_final: 0.6863 (t0) REVERT: C 232 ARG cc_start: 0.6349 (OUTLIER) cc_final: 0.5570 (mtp-110) REVERT: C 271 MET cc_start: 0.8251 (mtm) cc_final: 0.7750 (mtm) outliers start: 61 outliers final: 48 residues processed: 173 average time/residue: 0.0892 time to fit residues: 22.3135 Evaluate side-chains 176 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 123 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 553 GLN Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 0.0970 chunk 45 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 109 ASN B 340 GLN B 375 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.178902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118172 restraints weight = 12446.015| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.44 r_work: 0.2950 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11436 Z= 0.101 Angle : 0.529 9.796 15587 Z= 0.267 Chirality : 0.044 0.245 1714 Planarity : 0.004 0.036 2037 Dihedral : 5.289 55.606 1689 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.77 % Allowed : 23.33 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.22), residues: 1416 helix: 1.15 (0.30), residues: 350 sheet: 0.17 (0.32), residues: 280 loop : -1.04 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 319 TYR 0.019 0.001 TYR C 138 PHE 0.019 0.001 PHE A 413 TRP 0.010 0.001 TRP B 122 HIS 0.002 0.000 HIS C 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (11426) covalent geometry : angle 0.52566 / 0.27 (15561) SS BOND : bond 0.00174 / 0.09 ( 4) SS BOND : angle 0.73002 / 0.51 ( 8) hydrogen bonds : bond 0.02884 / 1.97 ( 377) hydrogen bonds : angle 4.70934 / 3.36 ( 1077) link_NAG-ASN : bond 0.00342 / 0.17 ( 6) link_NAG-ASN : angle 1.78511 / 1.14 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 135 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 41 PHE cc_start: 0.6176 (OUTLIER) cc_final: 0.4634 (t80) REVERT: A 56 ARG cc_start: 0.7536 (mmt90) cc_final: 0.6930 (mmt90) REVERT: A 497 ASP cc_start: 0.6510 (OUTLIER) cc_final: 0.6173 (t0) REVERT: B 50 ARG cc_start: 0.6451 (ttp-110) cc_final: 0.5739 (mtp-110) REVERT: B 109 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8739 (t0) REVERT: B 143 TYR cc_start: 0.8207 (m-80) cc_final: 0.7647 (m-10) REVERT: B 300 VAL cc_start: 0.8855 (m) cc_final: 0.8634 (t) REVERT: B 440 ASP cc_start: 0.7958 (t0) cc_final: 0.7605 (t0) REVERT: B 446 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6859 (tmt) REVERT: B 565 PHE cc_start: 0.7092 (m-80) cc_final: 0.6880 (m-10) REVERT: B 585 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6680 (mt) REVERT: C 104 ASP cc_start: 0.8376 (t0) cc_final: 0.7598 (t0) REVERT: C 232 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.5495 (mtp85) REVERT: C 271 MET cc_start: 0.8202 (mtm) cc_final: 0.7701 (mtm) outliers start: 55 outliers final: 45 residues processed: 169 average time/residue: 0.0897 time to fit residues: 21.8207 Evaluate side-chains 182 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 131 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 97 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 12 optimal weight: 0.0970 chunk 51 optimal weight: 0.0670 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 GLN B 375 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.176193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.115534 restraints weight = 12589.229| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.06 r_work: 0.2949 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11436 Z= 0.134 Angle : 0.551 9.780 15587 Z= 0.278 Chirality : 0.045 0.246 1714 Planarity : 0.004 0.035 2037 Dihedral : 5.152 55.575 1686 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.77 % Allowed : 22.90 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.22), residues: 1416 helix: 1.11 (0.30), residues: 352 sheet: 0.16 (0.32), residues: 278 loop : -1.06 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 112 TYR 0.020 0.001 TYR B 376 PHE 0.021 0.001 PHE A 413 TRP 0.007 0.001 TRP B 122 HIS 0.003 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.13 (11426) covalent geometry : angle 0.54771 / 0.28 (15561) SS BOND : bond 0.00264 / 0.14 ( 4) SS BOND : angle 0.71084 / 0.49 ( 8) hydrogen bonds : bond 0.03034 / 2.06 ( 377) hydrogen bonds : angle 4.73796 / 3.37 ( 1077) link_NAG-ASN : bond 0.00326 / 0.16 ( 6) link_NAG-ASN : angle 1.77936 / 1.13 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2404.57 seconds wall clock time: 41 minutes 47.22 seconds (2507.22 seconds total)