Starting phenix.real_space_refine on Tue Mar 3 23:12:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jbj_9791/03_2026/6jbj_9791_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jbj_9791/03_2026/6jbj_9791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6jbj_9791/03_2026/6jbj_9791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jbj_9791/03_2026/6jbj_9791.map" model { file = "/net/cci-nas-00/data/ceres_data/6jbj_9791/03_2026/6jbj_9791_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jbj_9791/03_2026/6jbj_9791_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 40 5.16 5 C 5914 2.51 5 N 1534 2.21 5 O 1672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9166 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4552 Classifications: {'peptide': 565} Link IDs: {'PTRANS': 19, 'TRANS': 545} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 3.50, per 1000 atoms: 0.38 Number of scatterers: 9166 At special positions: 0 Unit cell: (75.92, 73.84, 130, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 6 15.00 O 1672 8.00 N 1534 7.00 C 5914 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: 0.58 Conformation dependent library (CDL) restraints added in 261.3 milliseconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 63.9% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 18 through 32 removed outlier: 4.193A pdb=" N GLN A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 30 " --> pdb=" O GLN A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 61 removed outlier: 3.936A pdb=" N THR A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 46 " --> pdb=" O MET A 42 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 52 " --> pdb=" O CYS A 48 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 75 through 124 removed outlier: 3.877A pdb=" N THR A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 95 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 135 removed outlier: 3.786A pdb=" N ASN A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 159 removed outlier: 3.736A pdb=" N ASP A 149 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 180 removed outlier: 3.565A pdb=" N LEU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL A 172 " --> pdb=" O PRO A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 203 removed outlier: 3.930A pdb=" N TYR A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 231 removed outlier: 3.905A pdb=" N HIS A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 218 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 241 through 289 removed outlier: 4.281A pdb=" N MET A 247 " --> pdb=" O HIS A 243 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A 251 " --> pdb=" O MET A 247 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TRP A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TYR A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.608A pdb=" N PHE A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.778A pdb=" N VAL A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN A 346 " --> pdb=" O HIS A 342 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 426 through 435 removed outlier: 3.851A pdb=" N LEU A 430 " --> pdb=" O GLY A 426 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 475 removed outlier: 3.524A pdb=" N VAL A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 475 " --> pdb=" O ARG A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 486 Processing helix chain 'A' and resid 490 through 501 removed outlier: 3.719A pdb=" N LEU A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 509 removed outlier: 4.182A pdb=" N ALA A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 540 removed outlier: 3.858A pdb=" N GLN A 530 " --> pdb=" O PRO A 526 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG A 531 " --> pdb=" O GLY A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 removed outlier: 3.545A pdb=" N ILE A 565 " --> pdb=" O GLU A 561 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 585 removed outlier: 3.912A pdb=" N LYS A 584 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 32 removed outlier: 4.194A pdb=" N GLN B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE B 27 " --> pdb=" O ARG B 23 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL B 30 " --> pdb=" O GLN B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 61 removed outlier: 3.936A pdb=" N THR B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 46 " --> pdb=" O MET B 42 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU B 52 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 75 through 124 removed outlier: 3.877A pdb=" N THR B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 135 removed outlier: 3.786A pdb=" N ASN B 133 " --> pdb=" O TYR B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 removed outlier: 3.736A pdb=" N ASP B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 180 removed outlier: 3.565A pdb=" N LEU B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL B 172 " --> pdb=" O PRO B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 203 removed outlier: 3.930A pdb=" N TYR B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 231 removed outlier: 3.905A pdb=" N HIS B 214 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 218 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 241 through 289 removed outlier: 4.281A pdb=" N MET B 247 " --> pdb=" O HIS B 243 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG B 251 " --> pdb=" O MET B 247 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 259 " --> pdb=" O ARG B 255 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 262 " --> pdb=" O GLN B 258 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TRP B 269 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 270 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TYR B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.608A pdb=" N PHE B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 316 " --> pdb=" O LYS B 312 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 331 through 353 removed outlier: 3.778A pdb=" N VAL B 337 " --> pdb=" O THR B 333 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN B 346 " --> pdb=" O HIS B 342 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU B 349 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 426 through 435 removed outlier: 3.852A pdb=" N LEU B 430 " --> pdb=" O GLY B 426 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 475 removed outlier: 3.524A pdb=" N VAL B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 475 " --> pdb=" O ARG B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 486 Processing helix chain 'B' and resid 490 through 501 removed outlier: 3.719A pdb=" N LEU B 494 " --> pdb=" O ASP B 490 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 509 removed outlier: 4.182A pdb=" N ALA B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG B 508 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 540 removed outlier: 3.858A pdb=" N GLN B 530 " --> pdb=" O PRO B 526 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 531 " --> pdb=" O GLY B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 removed outlier: 3.545A pdb=" N ILE B 565 " --> pdb=" O GLU B 561 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY B 566 " --> pdb=" O LEU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 585 removed outlier: 3.912A pdb=" N LYS B 584 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 408 through 410 Processing sheet with id=AA2, first strand: chain 'A' and resid 456 through 458 removed outlier: 7.228A pdb=" N LEU A 457 " --> pdb=" O VAL A 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 408 through 410 Processing sheet with id=AA4, first strand: chain 'B' and resid 456 through 458 removed outlier: 7.227A pdb=" N LEU B 457 " --> pdb=" O VAL B 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 424 hydrogen bonds defined for protein. 1260 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: 1.19 Time building geometry restraints manager: 0.75 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: 2872 1.34 - 1.46: 1899 1.46 - 1.57: 4521 1.57 - 1.69: 10 1.69 - 1.81: 66 Bond restraints: 9368 Sorted by residual: bond pdb=" C SER B 302 " pdb=" N PRO B 303 " ideal model delta sigma weight residual 1.336 1.376 -0.040 9.80e-03 1.04e+04 1.64e+01 bond pdb=" C SER A 302 " pdb=" N PRO A 303 " ideal model delta sigma weight residual 1.336 1.375 -0.039 9.80e-03 1.04e+04 1.62e+01 bond pdb=" C LEU B 524 " pdb=" N SER B 525 " ideal model delta sigma weight residual 1.333 1.281 0.052 1.39e-02 5.18e+03 1.41e+01 bond pdb=" C LEU A 524 " pdb=" N SER A 525 " ideal model delta sigma weight residual 1.333 1.281 0.052 1.39e-02 5.18e+03 1.39e+01 bond pdb=" N PHE A 387 " pdb=" CA PHE A 387 " ideal model delta sigma weight residual 1.455 1.487 -0.033 1.29e-02 6.01e+03 6.45e+00 ... (remaining 9363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 12164 2.26 - 4.52: 449 4.52 - 6.78: 59 6.78 - 9.05: 24 9.05 - 11.31: 6 Bond angle restraints: 12702 Sorted by residual: angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 132.60 7.27 1.00e+00 1.00e+00 5.28e+01 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 132.63 7.24 1.00e+00 1.00e+00 5.25e+01 angle pdb=" C SER B 307 " pdb=" N THR B 308 " pdb=" CA THR B 308 " ideal model delta sigma weight residual 121.54 131.38 -9.84 1.91e+00 2.74e-01 2.65e+01 angle pdb=" C SER A 307 " pdb=" N THR A 308 " pdb=" CA THR A 308 " ideal model delta sigma weight residual 121.54 131.37 -9.83 1.91e+00 2.74e-01 2.65e+01 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 132.53 4.30 1.00e+00 1.00e+00 1.85e+01 ... (remaining 12697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 4813 17.67 - 35.33: 600 35.33 - 53.00: 135 53.00 - 70.66: 40 70.66 - 88.33: 10 Dihedral angle restraints: 5598 sinusoidal: 2316 harmonic: 3282 Sorted by residual: dihedral pdb=" CA MET A 227 " pdb=" C MET A 227 " pdb=" N GLN A 228 " pdb=" CA GLN A 228 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA MET B 227 " pdb=" C MET B 227 " pdb=" N GLN B 228 " pdb=" CA GLN B 228 " ideal model delta harmonic sigma weight residual 180.00 157.15 22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ILE A 475 " pdb=" C ILE A 475 " pdb=" N TYR A 476 " pdb=" CA TYR A 476 " ideal model delta harmonic sigma weight residual 180.00 -158.64 -21.36 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 5595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1017 0.057 - 0.114: 360 0.114 - 0.171: 49 0.171 - 0.228: 18 0.228 - 0.285: 4 Chirality restraints: 1448 Sorted by residual: chirality pdb=" CB ILE A 574 " pdb=" CA ILE A 574 " pdb=" CG1 ILE A 574 " pdb=" CG2 ILE A 574 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE B 574 " pdb=" CA ILE B 574 " pdb=" CG1 ILE B 574 " pdb=" CG2 ILE B 574 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE A 419 " pdb=" CA ILE A 419 " pdb=" CG1 ILE A 419 " pdb=" CG2 ILE A 419 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1445 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 167 " -0.055 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO A 168 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 167 " 0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO B 168 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 168 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 168 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 291 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO A 292 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 292 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 292 " -0.038 5.00e-02 4.00e+02 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1327 2.75 - 3.28: 9119 3.28 - 3.82: 15961 3.82 - 4.36: 19573 4.36 - 4.90: 31882 Nonbonded interactions: 77862 Sorted by model distance: nonbonded pdb=" O THR B 423 " pdb=" O1B ATP B 701 " model vdw 2.206 3.040 nonbonded pdb=" O THR A 423 " pdb=" O1B ATP A 701 " model vdw 2.206 3.040 nonbonded pdb=" O ILE A 291 " pdb=" OG SER A 295 " model vdw 2.312 3.040 nonbonded pdb=" O ILE B 291 " pdb=" OG SER B 295 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR A 108 " pdb=" OE1 GLN B 260 " model vdw 2.316 3.040 ... (remaining 77857 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.600 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 : 0.008 0.053 9368 Z= 0.361 Angle : 1.036 11.308 12702 Z= 0.555 Chirality : 0.059 0.285 1448 Planarity : 0.007 0.082 1580 Dihedral : 16.772 88.329 3490 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % 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: -6.19 (0.15), residues: 1122 helix: -4.17 (0.09), residues: 720 sheet: None (None), residues: 0 loop : -3.61 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 15 TYR 0.021 0.003 TYR B 319 PHE 0.032 0.003 PHE A 324 TRP 0.011 0.002 TRP A 520 HIS 0.004 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00782 ( 9368) covalent geometry : angle 1.03573 (12702) hydrogen bonds : bond 0.26520 ( 424) hydrogen bonds : angle 11.07489 ( 1260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9050 (mt) cc_final: 0.8779 (mt) REVERT: A 55 PHE cc_start: 0.7354 (t80) cc_final: 0.6893 (m-10) REVERT: A 68 TYR cc_start: 0.7741 (m-80) cc_final: 0.7426 (m-10) REVERT: A 217 LYS cc_start: 0.8455 (tttt) cc_final: 0.8248 (tttp) REVERT: A 247 MET cc_start: 0.7615 (mmt) cc_final: 0.7367 (mmt) REVERT: A 465 PHE cc_start: 0.9099 (m-80) cc_final: 0.8880 (m-10) REVERT: A 567 GLN cc_start: 0.7960 (mp10) cc_final: 0.7664 (pm20) REVERT: B 55 PHE cc_start: 0.7394 (t80) cc_final: 0.6830 (m-10) REVERT: B 315 PHE cc_start: 0.7541 (t80) cc_final: 0.7050 (t80) REVERT: B 388 LEU cc_start: 0.8653 (mt) cc_final: 0.8401 (mt) REVERT: B 422 ASN cc_start: 0.8214 (t0) cc_final: 0.7304 (m-40) REVERT: B 465 PHE cc_start: 0.9070 (m-80) cc_final: 0.8858 (m-10) REVERT: B 495 ARG cc_start: 0.8205 (ttt180) cc_final: 0.7997 (ttt90) REVERT: B 517 ASP cc_start: 0.7162 (m-30) cc_final: 0.6950 (m-30) REVERT: B 518 TRP cc_start: 0.7900 (m-10) cc_final: 0.7482 (m-10) REVERT: B 567 GLN cc_start: 0.7880 (mp10) cc_final: 0.7636 (pm20) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.0916 time to fit residues: 35.5044 Evaluate side-chains 198 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN A 201 ASN A 228 GLN ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN B 549 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.102528 restraints weight = 14650.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.105947 restraints weight = 7180.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.108068 restraints weight = 4620.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.109335 restraints weight = 3579.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.109884 restraints weight = 3091.478| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9368 Z= 0.168 Angle : 0.699 8.124 12702 Z= 0.360 Chirality : 0.043 0.146 1448 Planarity : 0.006 0.060 1580 Dihedral : 9.952 73.298 1310 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.08 % Allowed : 20.45 % Favored : 77.47 % 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: -4.39 (0.19), residues: 1122 helix: -2.46 (0.15), residues: 700 sheet: None (None), residues: 0 loop : -3.54 (0.24), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 145 TYR 0.013 0.001 TYR A 319 PHE 0.023 0.002 PHE B 451 TRP 0.016 0.002 TRP B 111 HIS 0.003 0.001 HIS B 342 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9368) covalent geometry : angle 0.69931 (12702) hydrogen bonds : bond 0.04889 ( 424) hydrogen bonds : angle 5.61210 ( 1260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 234 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9088 (mt) cc_final: 0.8869 (mt) REVERT: A 52 LEU cc_start: 0.9368 (tp) cc_final: 0.8999 (tp) REVERT: A 55 PHE cc_start: 0.7525 (t80) cc_final: 0.7047 (m-10) REVERT: A 84 PHE cc_start: 0.7887 (t80) cc_final: 0.7597 (t80) REVERT: A 217 LYS cc_start: 0.8548 (tttt) cc_final: 0.8184 (tttp) REVERT: A 234 GLU cc_start: 0.8561 (tp30) cc_final: 0.8174 (mm-30) REVERT: A 247 MET cc_start: 0.7728 (mmt) cc_final: 0.7480 (mmt) REVERT: A 271 TYR cc_start: 0.9073 (m-10) cc_final: 0.8779 (m-80) REVERT: A 312 LYS cc_start: 0.8235 (tmmt) cc_final: 0.7860 (ptmm) REVERT: A 422 ASN cc_start: 0.8193 (t0) cc_final: 0.7534 (m-40) REVERT: A 518 TRP cc_start: 0.7887 (m-10) cc_final: 0.7631 (m-10) REVERT: B 38 GLN cc_start: 0.7694 (tm-30) cc_final: 0.7360 (tm-30) REVERT: B 51 LEU cc_start: 0.9054 (mt) cc_final: 0.8689 (mp) REVERT: B 55 PHE cc_start: 0.7543 (t80) cc_final: 0.6783 (m-10) REVERT: B 230 ARG cc_start: 0.8699 (ttp80) cc_final: 0.8191 (ttp80) REVERT: B 234 GLU cc_start: 0.8504 (tp30) cc_final: 0.8146 (mm-30) REVERT: B 247 MET cc_start: 0.7848 (mmt) cc_final: 0.7639 (mmt) REVERT: B 312 LYS cc_start: 0.8234 (tmmt) cc_final: 0.7819 (ptmm) REVERT: B 315 PHE cc_start: 0.7655 (t80) cc_final: 0.7105 (t80) REVERT: B 422 ASN cc_start: 0.8049 (t0) cc_final: 0.7656 (m110) REVERT: B 465 PHE cc_start: 0.9090 (m-80) cc_final: 0.8880 (m-10) outliers start: 21 outliers final: 8 residues processed: 241 average time/residue: 0.0851 time to fit residues: 29.2720 Evaluate side-chains 202 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 194 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 92 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN ** B 567 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 = 0.3556 r_free = 0.3556 target = 0.130074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.103462 restraints weight = 14631.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.106876 restraints weight = 7115.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.109063 restraints weight = 4558.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.110340 restraints weight = 3491.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.110833 restraints weight = 3014.273| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9368 Z= 0.136 Angle : 0.641 8.529 12702 Z= 0.326 Chirality : 0.041 0.172 1448 Planarity : 0.004 0.045 1580 Dihedral : 8.428 79.677 1310 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 3.36 % Allowed : 22.73 % Favored : 73.91 % 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: -3.43 (0.21), residues: 1122 helix: -1.59 (0.17), residues: 706 sheet: -0.16 (1.20), residues: 20 loop : -3.56 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 252 TYR 0.010 0.001 TYR A 319 PHE 0.016 0.001 PHE A 222 TRP 0.022 0.002 TRP A 598 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9368) covalent geometry : angle 0.64067 (12702) hydrogen bonds : bond 0.04322 ( 424) hydrogen bonds : angle 4.93612 ( 1260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 228 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9355 (tp) cc_final: 0.9035 (tp) REVERT: A 55 PHE cc_start: 0.7586 (t80) cc_final: 0.6928 (m-10) REVERT: A 84 PHE cc_start: 0.7894 (t80) cc_final: 0.7657 (t80) REVERT: A 85 LEU cc_start: 0.9201 (tp) cc_final: 0.8948 (tt) REVERT: A 217 LYS cc_start: 0.8498 (tttt) cc_final: 0.8178 (tttp) REVERT: A 247 MET cc_start: 0.7777 (mmt) cc_final: 0.7528 (mmt) REVERT: A 268 LEU cc_start: 0.9339 (tt) cc_final: 0.9132 (tp) REVERT: A 312 LYS cc_start: 0.8121 (tmmt) cc_final: 0.7751 (ptmt) REVERT: A 324 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.8219 (t80) REVERT: A 422 ASN cc_start: 0.8138 (t0) cc_final: 0.7535 (m-40) REVERT: A 502 LEU cc_start: 0.9096 (pt) cc_final: 0.8792 (pp) REVERT: A 529 MET cc_start: 0.8486 (mtt) cc_final: 0.8227 (mtt) REVERT: A 561 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7788 (tm-30) REVERT: B 38 GLN cc_start: 0.7801 (tm-30) cc_final: 0.7373 (tm-30) REVERT: B 55 PHE cc_start: 0.7533 (t80) cc_final: 0.6791 (m-10) REVERT: B 85 LEU cc_start: 0.9175 (tp) cc_final: 0.8957 (tt) REVERT: B 247 MET cc_start: 0.7793 (mmt) cc_final: 0.7579 (mmt) REVERT: B 312 LYS cc_start: 0.8030 (tmmt) cc_final: 0.7699 (ptmt) REVERT: B 324 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.8263 (t80) REVERT: B 422 ASN cc_start: 0.7893 (t0) cc_final: 0.7492 (m-40) REVERT: B 502 LEU cc_start: 0.9074 (pt) cc_final: 0.8765 (pp) REVERT: B 561 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7809 (tm-30) outliers start: 34 outliers final: 16 residues processed: 250 average time/residue: 0.0854 time to fit residues: 30.6598 Evaluate side-chains 218 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 93 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 98 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 GLN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN B 215 GLN B 260 GLN B 549 GLN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.131153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.104444 restraints weight = 14738.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.107918 restraints weight = 7040.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.110066 restraints weight = 4457.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.111358 restraints weight = 3437.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.112045 restraints weight = 2969.774| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9368 Z= 0.138 Angle : 0.626 7.677 12702 Z= 0.318 Chirality : 0.042 0.154 1448 Planarity : 0.004 0.037 1580 Dihedral : 7.713 77.168 1310 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 3.66 % Allowed : 24.11 % Favored : 72.23 % 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: -2.91 (0.22), residues: 1122 helix: -1.17 (0.18), residues: 720 sheet: 0.01 (1.26), residues: 20 loop : -3.45 (0.25), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 15 TYR 0.010 0.001 TYR A 271 PHE 0.013 0.001 PHE A 222 TRP 0.019 0.001 TRP A 598 HIS 0.003 0.001 HIS B 226 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9368) covalent geometry : angle 0.62576 (12702) hydrogen bonds : bond 0.04080 ( 424) hydrogen bonds : angle 4.70442 ( 1260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7711 (tm-30) cc_final: 0.6996 (tm-30) REVERT: A 55 PHE cc_start: 0.7601 (t80) cc_final: 0.6897 (m-10) REVERT: A 84 PHE cc_start: 0.7872 (t80) cc_final: 0.7646 (t80) REVERT: A 85 LEU cc_start: 0.9214 (tp) cc_final: 0.8980 (tt) REVERT: A 136 ARG cc_start: 0.8299 (mmt-90) cc_final: 0.7800 (mpt180) REVERT: A 165 ILE cc_start: 0.8934 (tp) cc_final: 0.8723 (tp) REVERT: A 217 LYS cc_start: 0.8451 (tttt) cc_final: 0.8174 (tttp) REVERT: A 247 MET cc_start: 0.7696 (mmt) cc_final: 0.7394 (mmt) REVERT: A 268 LEU cc_start: 0.9313 (tt) cc_final: 0.9031 (tp) REVERT: A 312 LYS cc_start: 0.8117 (tmmt) cc_final: 0.7779 (ptmm) REVERT: A 324 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8277 (t80) REVERT: A 422 ASN cc_start: 0.8154 (t0) cc_final: 0.7553 (m110) REVERT: A 502 LEU cc_start: 0.9201 (pt) cc_final: 0.8890 (pp) REVERT: B 38 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7416 (tm-30) REVERT: B 51 LEU cc_start: 0.8995 (mt) cc_final: 0.8632 (mp) REVERT: B 55 PHE cc_start: 0.7597 (t80) cc_final: 0.6858 (m-10) REVERT: B 68 TYR cc_start: 0.7658 (m-10) cc_final: 0.7455 (m-10) REVERT: B 85 LEU cc_start: 0.9211 (tp) cc_final: 0.9005 (tt) REVERT: B 215 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: B 247 MET cc_start: 0.7698 (mmt) cc_final: 0.7473 (mmt) REVERT: B 312 LYS cc_start: 0.8095 (tmmt) cc_final: 0.7724 (ptmt) REVERT: B 324 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8305 (t80) REVERT: B 422 ASN cc_start: 0.7974 (t0) cc_final: 0.7548 (m110) REVERT: B 502 LEU cc_start: 0.9152 (pt) cc_final: 0.8858 (pp) outliers start: 37 outliers final: 23 residues processed: 240 average time/residue: 0.0753 time to fit residues: 26.9273 Evaluate side-chains 219 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 90 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN A 313 ASN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 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 = 0.3589 r_free = 0.3589 target = 0.131907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.105328 restraints weight = 14501.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.108753 restraints weight = 6937.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.110904 restraints weight = 4421.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.112140 restraints weight = 3414.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.112717 restraints weight = 2970.604| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9368 Z= 0.130 Angle : 0.611 6.596 12702 Z= 0.310 Chirality : 0.041 0.189 1448 Planarity : 0.004 0.036 1580 Dihedral : 7.116 73.057 1310 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.25 % Allowed : 25.30 % Favored : 70.45 % 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: -2.64 (0.23), residues: 1122 helix: -0.91 (0.18), residues: 718 sheet: -0.42 (1.15), residues: 20 loop : -3.38 (0.25), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 15 TYR 0.009 0.001 TYR A 271 PHE 0.014 0.001 PHE A 324 TRP 0.017 0.001 TRP B 598 HIS 0.002 0.001 HIS B 226 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9368) covalent geometry : angle 0.61111 (12702) hydrogen bonds : bond 0.03943 ( 424) hydrogen bonds : angle 4.56736 ( 1260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7778 (tm-30) cc_final: 0.7183 (tm-30) REVERT: A 55 PHE cc_start: 0.7609 (t80) cc_final: 0.6877 (m-10) REVERT: A 85 LEU cc_start: 0.9222 (tp) cc_final: 0.8986 (tt) REVERT: A 136 ARG cc_start: 0.8315 (mmt-90) cc_final: 0.7800 (mpt180) REVERT: A 165 ILE cc_start: 0.8912 (tp) cc_final: 0.8695 (tp) REVERT: A 193 TYR cc_start: 0.8268 (t80) cc_final: 0.7663 (t80) REVERT: A 217 LYS cc_start: 0.8391 (tttt) cc_final: 0.8128 (tttp) REVERT: A 247 MET cc_start: 0.7611 (mmt) cc_final: 0.7330 (mmt) REVERT: A 268 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9089 (tp) REVERT: A 312 LYS cc_start: 0.8147 (tmmt) cc_final: 0.7769 (ptmm) REVERT: A 324 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8287 (t80) REVERT: A 422 ASN cc_start: 0.8159 (t0) cc_final: 0.7568 (m110) REVERT: A 502 LEU cc_start: 0.9190 (pt) cc_final: 0.8912 (pp) REVERT: A 521 TYR cc_start: 0.8683 (m-80) cc_final: 0.8475 (m-80) REVERT: A 529 MET cc_start: 0.8447 (mtt) cc_final: 0.8034 (mtt) REVERT: A 561 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7784 (tm-30) REVERT: A 567 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7242 (pt0) REVERT: B 55 PHE cc_start: 0.7563 (t80) cc_final: 0.6818 (m-10) REVERT: B 68 TYR cc_start: 0.7754 (m-10) cc_final: 0.7539 (m-10) REVERT: B 193 TYR cc_start: 0.8215 (t80) cc_final: 0.7584 (t80) REVERT: B 312 LYS cc_start: 0.8080 (tmmt) cc_final: 0.7741 (ptmt) REVERT: B 324 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.8314 (t80) REVERT: B 422 ASN cc_start: 0.7993 (t0) cc_final: 0.7515 (m110) REVERT: B 502 LEU cc_start: 0.9178 (pt) cc_final: 0.8895 (pp) REVERT: B 529 MET cc_start: 0.8486 (mtt) cc_final: 0.8042 (mtt) REVERT: B 561 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7838 (tm-30) REVERT: B 567 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7282 (pt0) outliers start: 43 outliers final: 21 residues processed: 240 average time/residue: 0.0795 time to fit residues: 27.9997 Evaluate side-chains 221 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 GLN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.099403 restraints weight = 14735.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.102663 restraints weight = 7264.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.104720 restraints weight = 4704.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.105969 restraints weight = 3650.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.106546 restraints weight = 3160.949| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9368 Z= 0.212 Angle : 0.660 7.836 12702 Z= 0.336 Chirality : 0.044 0.181 1448 Planarity : 0.004 0.036 1580 Dihedral : 6.862 70.648 1310 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 5.04 % Allowed : 24.11 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.23), residues: 1122 helix: -0.79 (0.19), residues: 724 sheet: -0.97 (1.06), residues: 20 loop : -3.37 (0.25), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 15 TYR 0.011 0.001 TYR A 476 PHE 0.019 0.001 PHE A 324 TRP 0.023 0.001 TRP B 598 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 9368) covalent geometry : angle 0.65967 (12702) hydrogen bonds : bond 0.04152 ( 424) hydrogen bonds : angle 4.65303 ( 1260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 209 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7124 (tm-30) REVERT: A 55 PHE cc_start: 0.7602 (t80) cc_final: 0.6927 (m-10) REVERT: A 83 THR cc_start: 0.8496 (t) cc_final: 0.8214 (t) REVERT: A 85 LEU cc_start: 0.9234 (tp) cc_final: 0.8988 (tt) REVERT: A 165 ILE cc_start: 0.8945 (tp) cc_final: 0.8719 (tp) REVERT: A 217 LYS cc_start: 0.8505 (tttt) cc_final: 0.8200 (tttp) REVERT: A 227 MET cc_start: 0.8004 (ptp) cc_final: 0.7644 (ptp) REVERT: A 247 MET cc_start: 0.7560 (mmt) cc_final: 0.7294 (mmt) REVERT: A 312 LYS cc_start: 0.8190 (tmmt) cc_final: 0.7843 (ptmm) REVERT: A 502 LEU cc_start: 0.9295 (pt) cc_final: 0.8991 (pp) REVERT: A 517 ASP cc_start: 0.7065 (m-30) cc_final: 0.6791 (m-30) REVERT: A 521 TYR cc_start: 0.8716 (m-80) cc_final: 0.8467 (m-80) REVERT: A 567 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7137 (mt0) REVERT: B 55 PHE cc_start: 0.7594 (t80) cc_final: 0.6833 (m-10) REVERT: B 189 SER cc_start: 0.8447 (t) cc_final: 0.8224 (p) REVERT: B 312 LYS cc_start: 0.8138 (tmmt) cc_final: 0.7732 (ptmt) REVERT: B 406 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7412 (t0) REVERT: B 422 ASN cc_start: 0.8148 (t0) cc_final: 0.7553 (m110) REVERT: B 502 LEU cc_start: 0.9288 (pt) cc_final: 0.8992 (pp) REVERT: B 521 TYR cc_start: 0.8719 (m-80) cc_final: 0.8463 (m-80) REVERT: B 529 MET cc_start: 0.8535 (mtt) cc_final: 0.8083 (mtt) REVERT: B 567 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7124 (mt0) outliers start: 51 outliers final: 31 residues processed: 242 average time/residue: 0.0759 time to fit residues: 27.0692 Evaluate side-chains 226 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 319 TYR Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN A 549 GLN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.126505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.100047 restraints weight = 14851.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.103334 restraints weight = 7256.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.105430 restraints weight = 4653.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.106500 restraints weight = 3589.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.107304 restraints weight = 3138.548| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9368 Z= 0.185 Angle : 0.664 8.144 12702 Z= 0.336 Chirality : 0.043 0.185 1448 Planarity : 0.004 0.033 1580 Dihedral : 6.793 69.055 1310 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.25 % Allowed : 25.00 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.23), residues: 1122 helix: -0.75 (0.19), residues: 728 sheet: -1.07 (1.07), residues: 20 loop : -3.33 (0.26), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 15 TYR 0.011 0.001 TYR B 476 PHE 0.034 0.001 PHE A 324 TRP 0.035 0.001 TRP B 598 HIS 0.003 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 9368) covalent geometry : angle 0.66426 (12702) hydrogen bonds : bond 0.04094 ( 424) hydrogen bonds : angle 4.60980 ( 1260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 205 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7143 (tm-30) REVERT: A 55 PHE cc_start: 0.7594 (t80) cc_final: 0.6936 (m-10) REVERT: A 83 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8240 (t) REVERT: A 85 LEU cc_start: 0.9233 (tp) cc_final: 0.8992 (tt) REVERT: A 165 ILE cc_start: 0.8945 (tp) cc_final: 0.8718 (tp) REVERT: A 217 LYS cc_start: 0.8466 (tttt) cc_final: 0.8265 (tttp) REVERT: A 227 MET cc_start: 0.7839 (ptp) cc_final: 0.7559 (ppp) REVERT: A 247 MET cc_start: 0.7654 (mmt) cc_final: 0.7415 (mmt) REVERT: A 312 LYS cc_start: 0.8179 (tmmt) cc_final: 0.7850 (ptmm) REVERT: A 502 LEU cc_start: 0.9288 (pt) cc_final: 0.8964 (pp) REVERT: A 517 ASP cc_start: 0.7100 (m-30) cc_final: 0.6817 (m-30) REVERT: A 521 TYR cc_start: 0.8677 (m-80) cc_final: 0.8424 (m-80) REVERT: A 529 MET cc_start: 0.8507 (mtt) cc_final: 0.8038 (mtt) REVERT: A 567 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7053 (mt0) REVERT: B 55 PHE cc_start: 0.7610 (t80) cc_final: 0.6871 (m-10) REVERT: B 83 THR cc_start: 0.8449 (t) cc_final: 0.8174 (t) REVERT: B 85 LEU cc_start: 0.9237 (tp) cc_final: 0.9019 (tt) REVERT: B 422 ASN cc_start: 0.8183 (t0) cc_final: 0.7627 (m110) REVERT: B 502 LEU cc_start: 0.9263 (pt) cc_final: 0.8971 (pp) REVERT: B 517 ASP cc_start: 0.7087 (m-30) cc_final: 0.6821 (m-30) REVERT: B 521 TYR cc_start: 0.8703 (m-80) cc_final: 0.8456 (m-80) REVERT: B 529 MET cc_start: 0.8568 (mtt) cc_final: 0.8140 (mtt) REVERT: B 567 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7187 (mt0) outliers start: 43 outliers final: 30 residues processed: 233 average time/residue: 0.0761 time to fit residues: 26.5617 Evaluate side-chains 227 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 111 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 46 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.130321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.104041 restraints weight = 14505.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.107471 restraints weight = 6893.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.109619 restraints weight = 4352.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.110849 restraints weight = 3339.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.111415 restraints weight = 2891.126| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9368 Z= 0.135 Angle : 0.667 15.768 12702 Z= 0.331 Chirality : 0.042 0.260 1448 Planarity : 0.004 0.033 1580 Dihedral : 6.697 66.175 1310 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.96 % Allowed : 26.98 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.23), residues: 1122 helix: -0.62 (0.19), residues: 730 sheet: -0.91 (1.10), residues: 20 loop : -3.33 (0.25), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 15 TYR 0.010 0.001 TYR B 271 PHE 0.028 0.001 PHE A 324 TRP 0.019 0.001 TRP B 598 HIS 0.003 0.001 HIS B 226 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9368) covalent geometry : angle 0.66664 (12702) hydrogen bonds : bond 0.03941 ( 424) hydrogen bonds : angle 4.54979 ( 1260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7475 (tm-30) REVERT: A 55 PHE cc_start: 0.7571 (t80) cc_final: 0.6870 (m-10) REVERT: A 83 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8164 (t) REVERT: A 85 LEU cc_start: 0.9233 (tp) cc_final: 0.8987 (tt) REVERT: A 165 ILE cc_start: 0.8917 (tp) cc_final: 0.8685 (tp) REVERT: A 193 TYR cc_start: 0.8200 (t80) cc_final: 0.7472 (t80) REVERT: A 217 LYS cc_start: 0.8435 (tttt) cc_final: 0.8130 (tttp) REVERT: A 234 GLU cc_start: 0.8544 (tp30) cc_final: 0.8339 (tp30) REVERT: A 247 MET cc_start: 0.7656 (mmt) cc_final: 0.7427 (mmt) REVERT: A 312 LYS cc_start: 0.8152 (tmmt) cc_final: 0.7892 (ptmm) REVERT: A 422 ASN cc_start: 0.8177 (t0) cc_final: 0.7821 (m110) REVERT: A 502 LEU cc_start: 0.9253 (pt) cc_final: 0.8936 (pp) REVERT: A 517 ASP cc_start: 0.7011 (m-30) cc_final: 0.6743 (m-30) REVERT: A 521 TYR cc_start: 0.8627 (m-80) cc_final: 0.8411 (m-80) REVERT: A 561 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7832 (tm-30) REVERT: A 567 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7137 (mt0) REVERT: B 55 PHE cc_start: 0.7577 (t80) cc_final: 0.6835 (m-10) REVERT: B 83 THR cc_start: 0.8355 (t) cc_final: 0.8098 (t) REVERT: B 85 LEU cc_start: 0.9243 (tp) cc_final: 0.9021 (tt) REVERT: B 189 SER cc_start: 0.8634 (p) cc_final: 0.8240 (t) REVERT: B 193 TYR cc_start: 0.8167 (t80) cc_final: 0.7438 (t80) REVERT: B 234 GLU cc_start: 0.8521 (tp30) cc_final: 0.8296 (tp30) REVERT: B 422 ASN cc_start: 0.8127 (t0) cc_final: 0.7569 (m110) REVERT: B 502 LEU cc_start: 0.9243 (pt) cc_final: 0.8934 (pp) REVERT: B 521 TYR cc_start: 0.8655 (m-80) cc_final: 0.8399 (m-80) REVERT: B 529 MET cc_start: 0.8519 (mtt) cc_final: 0.8104 (mtt) REVERT: B 561 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7852 (tm-30) REVERT: B 567 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7153 (mt0) outliers start: 30 outliers final: 24 residues processed: 233 average time/residue: 0.0761 time to fit residues: 26.0745 Evaluate side-chains 229 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 15 optimal weight: 0.0770 chunk 18 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN A 473 GLN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.128565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.101800 restraints weight = 14740.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.105170 restraints weight = 7137.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.107242 restraints weight = 4552.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.108329 restraints weight = 3516.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.109092 restraints weight = 3074.828| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9368 Z= 0.168 Angle : 0.651 6.609 12702 Z= 0.329 Chirality : 0.043 0.354 1448 Planarity : 0.004 0.034 1580 Dihedral : 6.628 64.973 1310 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.26 % Allowed : 26.98 % Favored : 69.76 % 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: -2.18 (0.23), residues: 1122 helix: -0.55 (0.19), residues: 730 sheet: -1.04 (1.08), residues: 20 loop : -3.26 (0.25), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 15 TYR 0.012 0.001 TYR B 68 PHE 0.028 0.001 PHE A 324 TRP 0.022 0.002 TRP A 111 HIS 0.003 0.001 HIS B 226 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9368) covalent geometry : angle 0.65095 (12702) hydrogen bonds : bond 0.03970 ( 424) hydrogen bonds : angle 4.49292 ( 1260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7496 (tm-30) REVERT: A 55 PHE cc_start: 0.7584 (t80) cc_final: 0.6925 (m-10) REVERT: A 85 LEU cc_start: 0.9244 (tp) cc_final: 0.9006 (tt) REVERT: A 165 ILE cc_start: 0.8923 (tp) cc_final: 0.8689 (tp) REVERT: A 193 TYR cc_start: 0.8263 (t80) cc_final: 0.7557 (t80) REVERT: A 217 LYS cc_start: 0.8478 (tttt) cc_final: 0.8192 (tttp) REVERT: A 234 GLU cc_start: 0.8583 (tp30) cc_final: 0.8360 (tp30) REVERT: A 247 MET cc_start: 0.7720 (mmt) cc_final: 0.7497 (mmt) REVERT: A 312 LYS cc_start: 0.8205 (tmmt) cc_final: 0.7910 (ptmm) REVERT: A 422 ASN cc_start: 0.8183 (t0) cc_final: 0.7838 (m110) REVERT: A 502 LEU cc_start: 0.9290 (pt) cc_final: 0.8984 (pp) REVERT: A 517 ASP cc_start: 0.7058 (m-30) cc_final: 0.6795 (m-30) REVERT: A 561 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7844 (tm-30) REVERT: A 567 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7126 (mt0) REVERT: B 38 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7600 (tm-30) REVERT: B 55 PHE cc_start: 0.7616 (t80) cc_final: 0.6839 (m-10) REVERT: B 85 LEU cc_start: 0.9226 (tp) cc_final: 0.9001 (tt) REVERT: B 189 SER cc_start: 0.8769 (p) cc_final: 0.8269 (t) REVERT: B 193 TYR cc_start: 0.8241 (t80) cc_final: 0.7525 (t80) REVERT: B 234 GLU cc_start: 0.8568 (tp30) cc_final: 0.8318 (tp30) REVERT: B 293 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7172 (tt) REVERT: B 422 ASN cc_start: 0.8181 (t0) cc_final: 0.7618 (m110) REVERT: B 502 LEU cc_start: 0.9279 (pt) cc_final: 0.8968 (pp) REVERT: B 517 ASP cc_start: 0.7051 (m-30) cc_final: 0.6768 (m-30) REVERT: B 521 TYR cc_start: 0.8725 (m-80) cc_final: 0.8461 (m-80) REVERT: B 529 MET cc_start: 0.8563 (mtt) cc_final: 0.8135 (mtt) REVERT: B 561 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7854 (tm-30) REVERT: B 567 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7154 (mt0) outliers start: 33 outliers final: 26 residues processed: 232 average time/residue: 0.0765 time to fit residues: 26.0809 Evaluate side-chains 233 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 102 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 0.3980 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 35 optimal weight: 0.1980 chunk 93 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.102739 restraints weight = 14649.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.106158 restraints weight = 7010.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.108208 restraints weight = 4440.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.109430 restraints weight = 3431.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109827 restraints weight = 2977.100| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9368 Z= 0.156 Angle : 0.646 6.980 12702 Z= 0.325 Chirality : 0.042 0.229 1448 Planarity : 0.004 0.034 1580 Dihedral : 6.594 64.769 1310 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.96 % Allowed : 27.37 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.23), residues: 1122 helix: -0.48 (0.19), residues: 722 sheet: -1.05 (1.08), residues: 20 loop : -3.25 (0.25), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 15 TYR 0.014 0.001 TYR A 271 PHE 0.028 0.001 PHE A 324 TRP 0.021 0.001 TRP B 598 HIS 0.003 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9368) covalent geometry : angle 0.64626 (12702) hydrogen bonds : bond 0.03931 ( 424) hydrogen bonds : angle 4.47138 ( 1260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7945 (tm-30) cc_final: 0.7497 (tm-30) REVERT: A 55 PHE cc_start: 0.7574 (t80) cc_final: 0.6922 (m-10) REVERT: A 85 LEU cc_start: 0.9253 (tp) cc_final: 0.9003 (tt) REVERT: A 165 ILE cc_start: 0.8923 (tp) cc_final: 0.8686 (tp) REVERT: A 193 TYR cc_start: 0.8263 (t80) cc_final: 0.7448 (t80) REVERT: A 217 LYS cc_start: 0.8460 (tttt) cc_final: 0.8179 (tttp) REVERT: A 247 MET cc_start: 0.7703 (mmt) cc_final: 0.7495 (mmt) REVERT: A 312 LYS cc_start: 0.8235 (tmmt) cc_final: 0.7939 (ptmm) REVERT: A 422 ASN cc_start: 0.8136 (t0) cc_final: 0.7757 (m110) REVERT: A 502 LEU cc_start: 0.9292 (pt) cc_final: 0.8977 (pp) REVERT: A 517 ASP cc_start: 0.7040 (m-30) cc_final: 0.6787 (m-30) REVERT: A 567 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7141 (mt0) REVERT: B 55 PHE cc_start: 0.7590 (t80) cc_final: 0.6853 (m-10) REVERT: B 85 LEU cc_start: 0.9230 (tp) cc_final: 0.9007 (tt) REVERT: B 189 SER cc_start: 0.8766 (p) cc_final: 0.8257 (t) REVERT: B 193 TYR cc_start: 0.8233 (t80) cc_final: 0.7525 (t80) REVERT: B 234 GLU cc_start: 0.8534 (tp30) cc_final: 0.8300 (tp30) REVERT: B 293 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7245 (tt) REVERT: B 422 ASN cc_start: 0.8179 (t0) cc_final: 0.7615 (m110) REVERT: B 502 LEU cc_start: 0.9269 (pt) cc_final: 0.8957 (pp) REVERT: B 517 ASP cc_start: 0.7034 (m-30) cc_final: 0.6776 (m-30) REVERT: B 521 TYR cc_start: 0.8691 (m-80) cc_final: 0.8466 (m-80) REVERT: B 529 MET cc_start: 0.8571 (mtt) cc_final: 0.8142 (mtt) REVERT: B 567 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7138 (mt0) outliers start: 30 outliers final: 27 residues processed: 229 average time/residue: 0.0811 time to fit residues: 27.3642 Evaluate side-chains 233 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 0.0970 chunk 2 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 37 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN A 461 GLN A 549 GLN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN B 461 GLN B 549 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.131387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105462 restraints weight = 14509.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.108815 restraints weight = 6855.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.110907 restraints weight = 4337.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.112116 restraints weight = 3342.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.112524 restraints weight = 2900.365| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9368 Z= 0.125 Angle : 0.652 11.553 12702 Z= 0.323 Chirality : 0.041 0.191 1448 Planarity : 0.004 0.036 1580 Dihedral : 6.521 63.668 1310 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.16 % Allowed : 27.67 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.24), residues: 1122 helix: -0.38 (0.19), residues: 730 sheet: -0.87 (1.12), residues: 20 loop : -3.20 (0.26), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 15 TYR 0.010 0.001 TYR B 68 PHE 0.025 0.001 PHE B 324 TRP 0.015 0.001 TRP B 598 HIS 0.007 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9368) covalent geometry : angle 0.65189 (12702) hydrogen bonds : bond 0.03781 ( 424) hydrogen bonds : angle 4.39877 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1422.63 seconds wall clock time: 25 minutes 22.69 seconds (1522.69 seconds total)