Starting phenix.real_space_refine on Wed Jul 30 15:20:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fm9_50550/07_2025/9fm9_50550.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fm9_50550/07_2025/9fm9_50550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fm9_50550/07_2025/9fm9_50550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fm9_50550/07_2025/9fm9_50550.map" model { file = "/net/cci-nas-00/data/ceres_data/9fm9_50550/07_2025/9fm9_50550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fm9_50550/07_2025/9fm9_50550.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 71 5.16 5 C 8109 2.51 5 N 2192 2.21 5 O 2390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12764 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3847 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 23, 'TRANS': 475} Chain: "B" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3837 Classifications: {'peptide': 498} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 474} Chain: "C" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3504 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 22, 'TRANS': 432} Chain breaks: 2 Chain: "D" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1574 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain breaks: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.90, per 1000 atoms: 0.62 Number of scatterers: 12764 At special positions: 0 Unit cell: (108.68, 113.696, 103.664, 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) K 2 19.00 S 71 16.00 O 2390 8.00 N 2192 7.00 C 8109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 1.7 seconds 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3002 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 14 sheets defined 43.7% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 56 through 75 removed outlier: 3.748A pdb=" N ILE A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 95 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 111 through 136 removed outlier: 5.476A pdb=" N LEU A 120 " --> pdb=" O MET A 116 " (cutoff:3.500A) Proline residue: A 121 - end of helix Processing helix chain 'A' and resid 168 through 183 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 196 through 207 removed outlier: 3.894A pdb=" N MET A 200 " --> pdb=" O PRO A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 282 through 294 Processing helix chain 'A' and resid 295 through 301 removed outlier: 6.068A pdb=" N ASN A 298 " --> pdb=" O PHE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'A' and resid 347 through 364 Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.584A pdb=" N GLY A 383 " --> pdb=" O GLU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.574A pdb=" N CYS A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 489 Processing helix chain 'B' and resid 58 through 76 removed outlier: 4.463A pdb=" N GLU B 72 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LYS B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 96 removed outlier: 3.517A pdb=" N ASN B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 118 through 137 removed outlier: 3.759A pdb=" N ARG B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 183 removed outlier: 3.767A pdb=" N LYS B 176 " --> pdb=" O MET B 172 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 178 " --> pdb=" O CYS B 174 " (cutoff:3.500A) Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 197 through 206 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 243 through 255 Processing helix chain 'B' and resid 282 through 293 removed outlier: 3.551A pdb=" N THR B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 301 removed outlier: 5.342A pdb=" N ASN B 298 " --> pdb=" O PHE B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 4.458A pdb=" N GLN B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 365 removed outlier: 3.625A pdb=" N LYS B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'C' and resid 58 through 75 removed outlier: 5.038A pdb=" N GLU C 72 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LYS C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 96 removed outlier: 3.661A pdb=" N ASN C 96 " --> pdb=" O ARG C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 114 through 119 removed outlier: 3.699A pdb=" N ALA C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP C 119 " --> pdb=" O THR C 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 114 through 119' Processing helix chain 'C' and resid 119 through 137 removed outlier: 3.660A pdb=" N ARG C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 183 Proline residue: C 179 - end of helix Processing helix chain 'C' and resid 197 through 207 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 225 through 231 removed outlier: 3.610A pdb=" N LEU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 283 through 293 Processing helix chain 'C' and resid 297 through 301 removed outlier: 3.662A pdb=" N GLY C 300 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 328 Processing helix chain 'C' and resid 347 through 365 removed outlier: 3.615A pdb=" N LYS C 351 " --> pdb=" O SER C 347 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 364 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C 365 " --> pdb=" O GLY C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 426 Processing helix chain 'C' and resid 440 through 451 Processing helix chain 'D' and resid 59 through 75 removed outlier: 4.281A pdb=" N LYS D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY D 75 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 96 Processing helix chain 'D' and resid 119 through 137 Processing helix chain 'D' and resid 170 through 184 Proline residue: D 179 - end of helix Processing helix chain 'D' and resid 200 through 210 removed outlier: 3.664A pdb=" N LEU D 205 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP D 208 " --> pdb=" O ASN D 204 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 210 " --> pdb=" O ILE D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 425 Processing helix chain 'D' and resid 443 through 450 Processing helix chain 'D' and resid 483 through 487 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 42 removed outlier: 6.220A pdb=" N PHE A 38 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLN A 51 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASN A 40 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 47 " --> pdb=" O THR A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 140 through 143 removed outlier: 7.941A pdb=" N VAL B 456 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASN A 495 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N THR B 458 " --> pdb=" O ASN A 495 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A 497 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLY B 433 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N SER B 269 " --> pdb=" O ARG B 308 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU B 310 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ASN B 271 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLN B 312 " --> pdb=" O ASN B 271 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N PHE B 273 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N CYS B 305 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N SER B 411 " --> pdb=" O CYS B 305 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N SER B 307 " --> pdb=" O SER B 411 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR B 413 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL B 309 " --> pdb=" O THR B 413 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N PHE B 415 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 311 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR B 390 " --> pdb=" O VAL B 410 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL B 412 " --> pdb=" O THR B 390 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 217 removed outlier: 6.463A pdb=" N VAL A 160 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LYS A 190 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN A 162 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 241 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 367 through 370 removed outlier: 6.268A pdb=" N ILE A 391 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL A 309 " --> pdb=" O THR A 413 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE A 415 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE A 311 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 141 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL D 456 " --> pdb=" O THR C 493 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN C 495 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N THR D 458 " --> pdb=" O ASN C 495 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU C 497 " --> pdb=" O THR D 458 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 20 through 21 removed outlier: 8.005A pdb=" N TYR B 21 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASN B 40 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN B 51 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE B 38 " --> pdb=" O GLN B 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 23 through 25 Processing sheet with id=AA7, first strand: chain 'B' and resid 215 through 217 removed outlier: 6.643A pdb=" N VAL B 160 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LYS B 190 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN B 162 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS B 237 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.208A pdb=" N PHE C 38 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLN C 51 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASN C 40 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 159 through 164 Processing sheet with id=AB1, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.766A pdb=" N ILE C 272 " --> pdb=" O TRP C 437 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA C 434 " --> pdb=" O TRP C 457 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR D 148 " --> pdb=" O ASP D 145 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA D 150 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN D 143 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 308 through 312 removed outlier: 6.376A pdb=" N VAL C 309 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N PHE C 415 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE C 311 " --> pdb=" O PHE C 415 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL C 412 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 159 through 161 removed outlier: 3.613A pdb=" N VAL D 160 " --> pdb=" O CYS D 186 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 272 through 273 removed outlier: 6.805A pdb=" N ILE D 272 " --> pdb=" O TRP D 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 310 through 311 555 hydrogen bonds defined for protein. 1578 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: 3.76 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4247 1.34 - 1.46: 2765 1.46 - 1.58: 5904 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 13036 Sorted by residual: bond pdb=" N LEU D 170 " pdb=" CA LEU D 170 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.32e-02 5.74e+03 7.35e+00 bond pdb=" N CYS D 174 " pdb=" CA CYS D 174 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.20e-02 6.94e+03 6.66e+00 bond pdb=" N LYS D 176 " pdb=" CA LYS D 176 " ideal model delta sigma weight residual 1.460 1.490 -0.030 1.22e-02 6.72e+03 6.11e+00 bond pdb=" N MET D 172 " pdb=" CA MET D 172 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.28e+00 bond pdb=" N LEU D 177 " pdb=" CA LEU D 177 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.09e+00 ... (remaining 13031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 17339 2.34 - 4.68: 263 4.68 - 7.03: 37 7.03 - 9.37: 5 9.37 - 11.71: 3 Bond angle restraints: 17647 Sorted by residual: angle pdb=" C GLU C 18 " pdb=" N GLU C 19 " pdb=" CA GLU C 19 " ideal model delta sigma weight residual 121.54 133.25 -11.71 1.91e+00 2.74e-01 3.76e+01 angle pdb=" C ARG B 336 " pdb=" N GLU B 337 " pdb=" CA GLU B 337 " ideal model delta sigma weight residual 121.54 113.24 8.30 1.91e+00 2.74e-01 1.89e+01 angle pdb=" C GLU A 280 " pdb=" N ASP A 281 " pdb=" CA ASP A 281 " ideal model delta sigma weight residual 121.54 129.00 -7.46 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C PHE C 17 " pdb=" N GLU C 18 " pdb=" CA GLU C 18 " ideal model delta sigma weight residual 121.71 116.35 5.36 1.39e+00 5.18e-01 1.49e+01 angle pdb=" N LYS B 474 " pdb=" CA LYS B 474 " pdb=" C LYS B 474 " ideal model delta sigma weight residual 108.23 103.25 4.98 1.38e+00 5.25e-01 1.30e+01 ... (remaining 17642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6891 17.99 - 35.98: 699 35.98 - 53.97: 125 53.97 - 71.96: 24 71.96 - 89.95: 11 Dihedral angle restraints: 7750 sinusoidal: 3055 harmonic: 4695 Sorted by residual: dihedral pdb=" CA SER B 338 " pdb=" C SER B 338 " pdb=" N ASP B 339 " pdb=" CA ASP B 339 " ideal model delta harmonic sigma weight residual 180.00 -154.94 -25.06 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA PRO C 196 " pdb=" C PRO C 196 " pdb=" N ALA C 197 " pdb=" CA ALA C 197 " ideal model delta harmonic sigma weight residual 180.00 155.50 24.50 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ARG A 20 " pdb=" C ARG A 20 " pdb=" N TYR A 21 " pdb=" CA TYR A 21 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 7747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1480 0.054 - 0.107: 384 0.107 - 0.161: 48 0.161 - 0.215: 6 0.215 - 0.269: 1 Chirality restraints: 1919 Sorted by residual: chirality pdb=" CB ILE B 141 " pdb=" CA ILE B 141 " pdb=" CG1 ILE B 141 " pdb=" CG2 ILE B 141 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE B 206 " pdb=" CA ILE B 206 " pdb=" CG1 ILE B 206 " pdb=" CG2 ILE B 206 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.76e-01 chirality pdb=" CB ILE B 342 " pdb=" CA ILE B 342 " pdb=" CG1 ILE B 342 " pdb=" CG2 ILE B 342 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.52e-01 ... (remaining 1916 not shown) Planarity restraints: 2308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 253 " -0.018 2.00e-02 2.50e+03 1.93e-02 7.49e+00 pdb=" CG TYR A 253 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR A 253 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 253 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 253 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 253 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 253 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 253 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 211 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO B 212 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 212 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 212 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 305 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO B 306 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 306 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 306 " 0.030 5.00e-02 4.00e+02 ... (remaining 2305 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.79: 3009 2.79 - 3.37: 14079 3.37 - 3.96: 25645 3.96 - 4.55: 37406 4.55 - 5.14: 54506 Nonbonded interactions: 134645 Sorted by model distance: nonbonded pdb=" O ILE A 44 " pdb=" OH TYR A 386 " model vdw 2.197 3.040 nonbonded pdb=" NH1 ARG B 135 " pdb=" OD1 ASP D 125 " model vdw 2.212 3.120 nonbonded pdb=" OG1 THR A 304 " pdb=" OH TYR A 464 " model vdw 2.224 3.040 nonbonded pdb=" OD2 ASP C 276 " pdb=" OG SER C 438 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR C 357 " pdb=" OE1 GLU C 403 " model vdw 2.238 3.040 ... (remaining 134640 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 11 through 238 or resid 266 through 469 or resid 482 throu \ gh 504)) selection = (chain 'B' and (resid 11 through 238 or resid 266 through 469 or resid 482 throu \ gh 504)) selection = chain 'C' } 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: 1.040 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.830 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13036 Z= 0.245 Angle : 0.735 11.709 17647 Z= 0.414 Chirality : 0.047 0.269 1919 Planarity : 0.005 0.055 2308 Dihedral : 15.081 89.951 4748 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.23 % Allowed : 0.84 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.20), residues: 1627 helix: -0.83 (0.19), residues: 655 sheet: -1.35 (0.29), residues: 335 loop : -1.73 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 437 HIS 0.022 0.003 HIS C 467 PHE 0.028 0.002 PHE A 130 TYR 0.048 0.003 TYR A 253 ARG 0.011 0.001 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.15984 ( 555) hydrogen bonds : angle 7.31058 ( 1578) covalent geometry : bond 0.00557 (13036) covalent geometry : angle 0.73516 (17647) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 191 time to evaluate : 1.438 Fit side-chains REVERT: B 36 ARG cc_start: 0.7326 (mtm-85) cc_final: 0.6780 (mtm180) REVERT: B 392 PHE cc_start: 0.8017 (m-80) cc_final: 0.7775 (m-80) REVERT: C 107 ASP cc_start: 0.7371 (t70) cc_final: 0.7115 (t70) outliers start: 3 outliers final: 0 residues processed: 192 average time/residue: 0.2938 time to fit residues: 80.0094 Evaluate side-chains 153 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 66 optimal weight: 0.0060 chunk 127 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN B 345 GLN B 495 ASN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.140994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.115865 restraints weight = 16324.797| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.69 r_work: 0.3255 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 13036 Z= 0.281 Angle : 0.714 9.329 17647 Z= 0.373 Chirality : 0.049 0.234 1919 Planarity : 0.005 0.052 2308 Dihedral : 5.799 79.146 1772 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.61 % Allowed : 9.79 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.20), residues: 1627 helix: -0.52 (0.19), residues: 649 sheet: -1.45 (0.29), residues: 331 loop : -1.59 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 74 HIS 0.019 0.002 HIS C 467 PHE 0.030 0.003 PHE A 130 TYR 0.040 0.002 TYR A 253 ARG 0.007 0.001 ARG A 455 Details of bonding type rmsd hydrogen bonds : bond 0.05645 ( 555) hydrogen bonds : angle 5.68835 ( 1578) covalent geometry : bond 0.00675 (13036) covalent geometry : angle 0.71354 (17647) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 1.326 Fit side-chains REVERT: A 104 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6958 (mm-30) REVERT: C 65 ASP cc_start: 0.7507 (m-30) cc_final: 0.7204 (m-30) REVERT: C 107 ASP cc_start: 0.8252 (t70) cc_final: 0.7991 (t70) outliers start: 8 outliers final: 7 residues processed: 169 average time/residue: 0.2759 time to fit residues: 65.8486 Evaluate side-chains 155 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 429 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 42 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 18 optimal weight: 0.0970 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 GLN A 396 ASN A 491 GLN B 325 GLN B 345 GLN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.146250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.121537 restraints weight = 16344.862| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.78 r_work: 0.3346 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13036 Z= 0.122 Angle : 0.559 7.860 17647 Z= 0.293 Chirality : 0.043 0.196 1919 Planarity : 0.004 0.049 2308 Dihedral : 5.164 73.543 1772 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.30 % Allowed : 11.54 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.21), residues: 1627 helix: 0.25 (0.20), residues: 653 sheet: -1.22 (0.29), residues: 329 loop : -1.39 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 74 HIS 0.008 0.001 HIS C 467 PHE 0.023 0.002 PHE A 130 TYR 0.042 0.001 TYR A 253 ARG 0.006 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 555) hydrogen bonds : angle 5.18889 ( 1578) covalent geometry : bond 0.00274 (13036) covalent geometry : angle 0.55915 (17647) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.7288 (m-80) cc_final: 0.6408 (m-80) REVERT: B 403 GLU cc_start: 0.5950 (OUTLIER) cc_final: 0.5532 (mt-10) REVERT: B 503 LYS cc_start: 0.8434 (mtmt) cc_final: 0.8174 (mmtm) REVERT: C 65 ASP cc_start: 0.7401 (m-30) cc_final: 0.7016 (m-30) REVERT: C 107 ASP cc_start: 0.8206 (t70) cc_final: 0.7885 (t70) REVERT: D 88 LYS cc_start: 0.7654 (mttm) cc_final: 0.7362 (mttt) outliers start: 17 outliers final: 8 residues processed: 191 average time/residue: 0.2814 time to fit residues: 76.2119 Evaluate side-chains 172 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 429 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 73 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 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 = 0.3743 r_free = 0.3743 target = 0.141809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.116530 restraints weight = 16398.217| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.69 r_work: 0.3269 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 13036 Z= 0.257 Angle : 0.642 7.939 17647 Z= 0.336 Chirality : 0.047 0.197 1919 Planarity : 0.005 0.048 2308 Dihedral : 5.462 78.292 1772 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.76 % Allowed : 15.21 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.21), residues: 1627 helix: 0.09 (0.20), residues: 649 sheet: -1.37 (0.29), residues: 331 loop : -1.40 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 74 HIS 0.011 0.002 HIS A 467 PHE 0.026 0.003 PHE A 130 TYR 0.041 0.002 TYR A 253 ARG 0.007 0.001 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.05054 ( 555) hydrogen bonds : angle 5.32137 ( 1578) covalent geometry : bond 0.00619 (13036) covalent geometry : angle 0.64238 (17647) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.486 Fit side-chains revert: symmetry clash REVERT: B 403 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5615 (mt-10) REVERT: C 65 ASP cc_start: 0.7482 (m-30) cc_final: 0.7134 (m-30) REVERT: C 107 ASP cc_start: 0.8248 (t70) cc_final: 0.8022 (t70) REVERT: C 402 GLN cc_start: 0.6885 (OUTLIER) cc_final: 0.6166 (mp10) outliers start: 23 outliers final: 14 residues processed: 176 average time/residue: 0.2740 time to fit residues: 68.8218 Evaluate side-chains 174 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 402 GLN Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain D residue 86 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 1 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.141812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.116457 restraints weight = 16464.050| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.71 r_work: 0.3269 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 13036 Z= 0.232 Angle : 0.630 8.171 17647 Z= 0.329 Chirality : 0.046 0.190 1919 Planarity : 0.005 0.047 2308 Dihedral : 5.483 78.471 1772 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.68 % Allowed : 16.06 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.21), residues: 1627 helix: 0.07 (0.20), residues: 649 sheet: -1.37 (0.29), residues: 329 loop : -1.40 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 74 HIS 0.010 0.002 HIS A 467 PHE 0.026 0.002 PHE A 130 TYR 0.046 0.002 TYR A 253 ARG 0.008 0.001 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04943 ( 555) hydrogen bonds : angle 5.30891 ( 1578) covalent geometry : bond 0.00555 (13036) covalent geometry : angle 0.62977 (17647) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: B 18 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6035 (mp0) REVERT: B 36 ARG cc_start: 0.7514 (mtm-85) cc_final: 0.7216 (mtm-85) REVERT: B 403 GLU cc_start: 0.6135 (OUTLIER) cc_final: 0.5570 (mt-10) REVERT: B 406 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.7826 (t80) REVERT: C 65 ASP cc_start: 0.7496 (m-30) cc_final: 0.7128 (m-30) REVERT: C 107 ASP cc_start: 0.8283 (t0) cc_final: 0.8044 (t70) REVERT: C 402 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.6305 (mp10) outliers start: 35 outliers final: 20 residues processed: 194 average time/residue: 0.2723 time to fit residues: 75.3112 Evaluate side-chains 184 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 402 GLN Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 81 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 58 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.142668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.117403 restraints weight = 16552.769| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.71 r_work: 0.3285 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 13036 Z= 0.189 Angle : 0.600 8.869 17647 Z= 0.313 Chirality : 0.045 0.161 1919 Planarity : 0.004 0.047 2308 Dihedral : 5.364 76.781 1772 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.22 % Allowed : 17.28 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.21), residues: 1627 helix: 0.21 (0.20), residues: 650 sheet: -1.38 (0.29), residues: 331 loop : -1.30 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 74 HIS 0.008 0.001 HIS C 467 PHE 0.024 0.002 PHE A 130 TYR 0.046 0.002 TYR A 253 ARG 0.006 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04646 ( 555) hydrogen bonds : angle 5.21034 ( 1578) covalent geometry : bond 0.00452 (13036) covalent geometry : angle 0.59954 (17647) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 2.257 Fit side-chains revert: symmetry clash REVERT: B 36 ARG cc_start: 0.7515 (mtm-85) cc_final: 0.7206 (mtm-85) REVERT: B 403 GLU cc_start: 0.6038 (OUTLIER) cc_final: 0.5503 (mt-10) REVERT: C 65 ASP cc_start: 0.7463 (m-30) cc_final: 0.7085 (m-30) REVERT: C 107 ASP cc_start: 0.8239 (t0) cc_final: 0.8020 (t70) REVERT: C 402 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.6254 (mp10) outliers start: 29 outliers final: 25 residues processed: 183 average time/residue: 0.3813 time to fit residues: 100.3785 Evaluate side-chains 185 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 3.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 402 GLN Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 136 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.143616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118474 restraints weight = 16316.762| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.70 r_work: 0.3299 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13036 Z= 0.164 Angle : 0.578 8.036 17647 Z= 0.302 Chirality : 0.044 0.151 1919 Planarity : 0.004 0.046 2308 Dihedral : 5.178 73.446 1772 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.91 % Allowed : 17.05 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.21), residues: 1627 helix: 0.34 (0.20), residues: 655 sheet: -1.32 (0.29), residues: 329 loop : -1.27 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 74 HIS 0.006 0.001 HIS C 467 PHE 0.021 0.002 PHE A 130 TYR 0.047 0.002 TYR A 253 ARG 0.006 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 555) hydrogen bonds : angle 5.10559 ( 1578) covalent geometry : bond 0.00390 (13036) covalent geometry : angle 0.57795 (17647) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 2.357 Fit side-chains REVERT: B 18 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6019 (mp0) REVERT: B 36 ARG cc_start: 0.7483 (mtm-85) cc_final: 0.7255 (mtm-85) REVERT: B 380 GLU cc_start: 0.7423 (tt0) cc_final: 0.7023 (pm20) REVERT: B 403 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5563 (mt-10) REVERT: C 65 ASP cc_start: 0.7457 (m-30) cc_final: 0.7074 (m-30) REVERT: C 107 ASP cc_start: 0.8214 (t0) cc_final: 0.7999 (t70) REVERT: C 402 GLN cc_start: 0.6770 (OUTLIER) cc_final: 0.6157 (mp10) REVERT: D 493 THR cc_start: 0.8143 (m) cc_final: 0.7934 (m) outliers start: 38 outliers final: 30 residues processed: 195 average time/residue: 0.3168 time to fit residues: 89.8387 Evaluate side-chains 193 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 402 GLN Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 272 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 88 optimal weight: 0.0570 chunk 135 optimal weight: 6.9990 chunk 156 optimal weight: 8.9990 chunk 55 optimal weight: 0.0070 chunk 95 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.143355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.118241 restraints weight = 16419.512| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.70 r_work: 0.3299 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13036 Z= 0.166 Angle : 0.581 7.873 17647 Z= 0.304 Chirality : 0.044 0.151 1919 Planarity : 0.004 0.046 2308 Dihedral : 5.151 73.345 1772 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.60 % Allowed : 17.35 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.21), residues: 1627 helix: 0.41 (0.20), residues: 654 sheet: -1.31 (0.29), residues: 329 loop : -1.21 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 74 HIS 0.006 0.001 HIS C 467 PHE 0.022 0.002 PHE A 130 TYR 0.047 0.002 TYR A 253 ARG 0.005 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 555) hydrogen bonds : angle 5.07663 ( 1578) covalent geometry : bond 0.00393 (13036) covalent geometry : angle 0.58147 (17647) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 1.385 Fit side-chains revert: symmetry clash REVERT: A 104 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6878 (mm-30) REVERT: B 18 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.5933 (mp0) REVERT: B 36 ARG cc_start: 0.7490 (mtm-85) cc_final: 0.7256 (mtm-85) REVERT: B 221 PHE cc_start: 0.7861 (m-10) cc_final: 0.7604 (m-80) REVERT: B 227 LYS cc_start: 0.7600 (tttm) cc_final: 0.7187 (mtpt) REVERT: B 403 GLU cc_start: 0.6021 (OUTLIER) cc_final: 0.5534 (mt-10) REVERT: C 65 ASP cc_start: 0.7465 (m-30) cc_final: 0.7087 (m-30) REVERT: C 107 ASP cc_start: 0.8230 (t0) cc_final: 0.8017 (t70) REVERT: C 402 GLN cc_start: 0.6815 (OUTLIER) cc_final: 0.6560 (mm110) REVERT: D 96 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7639 (t0) REVERT: D 174 CYS cc_start: 0.7681 (m) cc_final: 0.7294 (m) REVERT: D 493 THR cc_start: 0.8139 (m) cc_final: 0.7935 (m) outliers start: 34 outliers final: 29 residues processed: 196 average time/residue: 0.2790 time to fit residues: 78.4004 Evaluate side-chains 197 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 402 GLN Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 272 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.0980 chunk 85 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.143561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.118656 restraints weight = 16377.546| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.68 r_work: 0.3303 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13036 Z= 0.165 Angle : 0.576 7.858 17647 Z= 0.301 Chirality : 0.044 0.148 1919 Planarity : 0.004 0.046 2308 Dihedral : 5.139 73.621 1772 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.45 % Allowed : 17.89 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.21), residues: 1627 helix: 0.44 (0.20), residues: 654 sheet: -1.19 (0.28), residues: 343 loop : -1.22 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 74 HIS 0.006 0.001 HIS C 467 PHE 0.021 0.002 PHE A 130 TYR 0.047 0.002 TYR A 253 ARG 0.005 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 555) hydrogen bonds : angle 5.05595 ( 1578) covalent geometry : bond 0.00391 (13036) covalent geometry : angle 0.57571 (17647) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 1.549 Fit side-chains REVERT: A 104 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6895 (mm-30) REVERT: B 18 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.5994 (mp0) REVERT: B 36 ARG cc_start: 0.7485 (mtm-85) cc_final: 0.7255 (mtm-85) REVERT: B 227 LYS cc_start: 0.7585 (tttm) cc_final: 0.7173 (mtpt) REVERT: B 351 LYS cc_start: 0.6910 (mttt) cc_final: 0.6693 (mttt) REVERT: B 403 GLU cc_start: 0.6061 (OUTLIER) cc_final: 0.5567 (mt-10) REVERT: C 65 ASP cc_start: 0.7434 (m-30) cc_final: 0.7037 (m-30) REVERT: C 107 ASP cc_start: 0.8235 (t0) cc_final: 0.8028 (t70) REVERT: C 402 GLN cc_start: 0.6800 (OUTLIER) cc_final: 0.6547 (mm110) REVERT: D 96 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7659 (t0) REVERT: D 174 CYS cc_start: 0.7638 (m) cc_final: 0.7235 (m) outliers start: 32 outliers final: 28 residues processed: 194 average time/residue: 0.2806 time to fit residues: 77.2503 Evaluate side-chains 201 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 402 GLN Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 272 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 89 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 chunk 127 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.118909 restraints weight = 16360.967| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.71 r_work: 0.3307 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13036 Z= 0.156 Angle : 0.569 7.670 17647 Z= 0.297 Chirality : 0.044 0.147 1919 Planarity : 0.004 0.050 2308 Dihedral : 5.097 73.633 1772 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.37 % Allowed : 18.20 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1627 helix: 0.51 (0.20), residues: 654 sheet: -1.19 (0.28), residues: 345 loop : -1.20 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 74 HIS 0.005 0.001 HIS C 467 PHE 0.021 0.002 PHE A 130 TYR 0.048 0.002 TYR A 253 ARG 0.005 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04239 ( 555) hydrogen bonds : angle 5.02682 ( 1578) covalent geometry : bond 0.00369 (13036) covalent geometry : angle 0.56911 (17647) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 2.277 Fit side-chains REVERT: A 104 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6871 (mm-30) REVERT: B 18 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.5960 (mp0) REVERT: B 36 ARG cc_start: 0.7471 (mtm-85) cc_final: 0.7232 (mtm-85) REVERT: B 221 PHE cc_start: 0.7880 (m-10) cc_final: 0.7654 (m-80) REVERT: B 227 LYS cc_start: 0.7578 (tttm) cc_final: 0.7166 (mtpt) REVERT: B 351 LYS cc_start: 0.6833 (mttt) cc_final: 0.6430 (mttt) REVERT: B 403 GLU cc_start: 0.6048 (OUTLIER) cc_final: 0.5555 (mt-10) REVERT: B 503 LYS cc_start: 0.8425 (mtmt) cc_final: 0.8177 (mmtm) REVERT: C 65 ASP cc_start: 0.7421 (m-30) cc_final: 0.7023 (m-30) REVERT: C 402 GLN cc_start: 0.6807 (OUTLIER) cc_final: 0.6562 (mm110) REVERT: D 96 ASN cc_start: 0.8006 (OUTLIER) cc_final: 0.7680 (t0) REVERT: D 122 LEU cc_start: 0.6556 (mt) cc_final: 0.6207 (tt) REVERT: D 174 CYS cc_start: 0.7647 (m) cc_final: 0.7247 (m) outliers start: 31 outliers final: 27 residues processed: 193 average time/residue: 0.3350 time to fit residues: 92.3346 Evaluate side-chains 201 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 406 PHE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 402 GLN Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 272 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 156 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 1 optimal weight: 0.0270 chunk 95 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 151 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN D 489 HIS ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.141041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115952 restraints weight = 16442.104| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.69 r_work: 0.3263 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 13036 Z= 0.258 Angle : 0.655 8.193 17647 Z= 0.340 Chirality : 0.047 0.204 1919 Planarity : 0.005 0.045 2308 Dihedral : 5.460 77.834 1772 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.68 % Allowed : 18.20 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.21), residues: 1627 helix: 0.13 (0.20), residues: 656 sheet: -1.33 (0.29), residues: 329 loop : -1.24 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 74 HIS 0.008 0.002 HIS C 467 PHE 0.024 0.003 PHE A 130 TYR 0.049 0.002 TYR A 253 ARG 0.006 0.001 ARG C 455 Details of bonding type rmsd hydrogen bonds : bond 0.05023 ( 555) hydrogen bonds : angle 5.22962 ( 1578) covalent geometry : bond 0.00615 (13036) covalent geometry : angle 0.65537 (17647) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7525.12 seconds wall clock time: 136 minutes 33.17 seconds (8193.17 seconds total)