Starting phenix.real_space_refine on Thu Jul 2 20:53:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x0t_32924/07_2026/7x0t_32924.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x0t_32924/07_2026/7x0t_32924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x0t_32924/07_2026/7x0t_32924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x0t_32924/07_2026/7x0t_32924.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7x0t_32924/07_2026/7x0t_32924.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x0t_32924/07_2026/7x0t_32924.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x0t_32924/07_2026/7x0t_32924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x0t_32924/07_2026/7x0t_32924.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.030 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 49 5.16 5 C 6504 2.51 5 N 1796 2.21 5 O 1834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10189 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5051 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 22, 'TRANS': 610} Chain breaks: 1 Chain: "B" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5051 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 22, 'TRANS': 610} Chain breaks: 1 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'CO8': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.54, per 1000 atoms: 0.25 Number of scatterers: 10189 At special positions: 0 Unit cell: (75.53, 113.71, 154.38, 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 49 16.00 P 6 15.00 O 1834 8.00 N 1796 7.00 C 6504 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: 1.13 Conformation dependent library (CDL) restraints added in 426.4 milliseconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2372 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 3 sheets defined 48.6% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 69 through 77 removed outlier: 3.926A pdb=" N GLN A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 95 through 107 removed outlier: 3.611A pdb=" N SER A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ARG A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 139 removed outlier: 4.097A pdb=" N GLY A 131 " --> pdb=" O PRO A 127 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLN A 136 " --> pdb=" O TRP A 132 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP A 137 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 150 removed outlier: 3.656A pdb=" N VAL A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 200 through 213 removed outlier: 3.603A pdb=" N ALA A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.562A pdb=" N ASP A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 236 removed outlier: 3.627A pdb=" N ALA A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 276 through 289 removed outlier: 3.846A pdb=" N ARG A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 302 through 307 Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.527A pdb=" N PHE A 333 " --> pdb=" O MET A 329 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 removed outlier: 3.507A pdb=" N VAL A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 362 through 370 removed outlier: 3.911A pdb=" N LYS A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 379 through 398 removed outlier: 3.703A pdb=" N ALA A 384 " --> pdb=" O GLU A 380 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 404 through 406 No H-bonds generated for 'chain 'A' and resid 404 through 406' Processing helix chain 'A' and resid 407 through 429 removed outlier: 3.796A pdb=" N GLU A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A 414 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 508 through 513 removed outlier: 4.107A pdb=" N GLY A 512 " --> pdb=" O ASN A 509 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LYS A 513 " --> pdb=" O GLY A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 552 through 556 removed outlier: 3.525A pdb=" N GLN A 556 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.748A pdb=" N VAL A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 591 Processing helix chain 'A' and resid 606 through 621 removed outlier: 3.780A pdb=" N GLN A 611 " --> pdb=" O GLY A 607 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG A 612 " --> pdb=" O GLY A 608 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET A 618 " --> pdb=" O GLY A 614 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE A 619 " --> pdb=" O MET A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 650 Processing helix chain 'A' and resid 660 through 667 removed outlier: 3.881A pdb=" N TRP A 664 " --> pdb=" O PRO A 661 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS A 665 " --> pdb=" O SER A 662 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS A 667 " --> pdb=" O TRP A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 700 removed outlier: 4.186A pdb=" N LYS A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 720 removed outlier: 3.739A pdb=" N LEU A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 74 removed outlier: 3.693A pdb=" N LEU B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 removed outlier: 4.044A pdb=" N LEU B 81 " --> pdb=" O TRP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 103 removed outlier: 3.606A pdb=" N VAL B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 98 through 103' Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.846A pdb=" N ARG B 117 " --> pdb=" O ARG B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.868A pdb=" N GLN B 136 " --> pdb=" O TRP B 132 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TRP B 137 " --> pdb=" O GLN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 150 removed outlier: 3.754A pdb=" N VAL B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'B' and resid 201 through 217 removed outlier: 3.871A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN B 214 " --> pdb=" O HIS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.588A pdb=" N ASP B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 267 through 275 Processing helix chain 'B' and resid 278 through 289 removed outlier: 3.544A pdb=" N MET B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 287 " --> pdb=" O HIS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 300 through 305 removed outlier: 3.647A pdb=" N LEU B 305 " --> pdb=" O VAL B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 removed outlier: 3.655A pdb=" N SER B 315 " --> pdb=" O ASP B 312 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B 316 " --> pdb=" O LEU B 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 312 through 316' Processing helix chain 'B' and resid 317 through 324 Processing helix chain 'B' and resid 339 through 344 removed outlier: 3.563A pdb=" N LEU B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 353 Processing helix chain 'B' and resid 362 through 371 Processing helix chain 'B' and resid 373 through 394 removed outlier: 3.881A pdb=" N SER B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 421 removed outlier: 4.879A pdb=" N ARG B 418 " --> pdb=" O GLY B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 429 removed outlier: 4.052A pdb=" N GLU B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 513 through 521 removed outlier: 4.070A pdb=" N PHE B 517 " --> pdb=" O LYS B 513 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.949A pdb=" N VAL B 557 " --> pdb=" O ARG B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 583 removed outlier: 3.503A pdb=" N ILE B 579 " --> pdb=" O ASP B 575 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 592 removed outlier: 3.545A pdb=" N GLU B 592 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 621 removed outlier: 3.649A pdb=" N ARG B 612 " --> pdb=" O GLY B 608 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET B 615 " --> pdb=" O GLN B 611 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET B 618 " --> pdb=" O GLY B 614 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 619 " --> pdb=" O MET B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 650 removed outlier: 4.881A pdb=" N ILE B 643 " --> pdb=" O VAL B 639 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 644 " --> pdb=" O GLU B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 665 removed outlier: 3.565A pdb=" N LEU B 663 " --> pdb=" O ARG B 660 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS B 665 " --> pdb=" O SER B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 704 Processing helix chain 'B' and resid 707 through 721 removed outlier: 4.100A pdb=" N ARG B 712 " --> pdb=" O LYS B 708 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 715 " --> pdb=" O ARG B 711 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 481 through 482 removed outlier: 6.716A pdb=" N ILE A 481 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 504 through 505 Processing sheet with id=AA3, first strand: chain 'B' and resid 541 through 542 removed outlier: 3.631A pdb=" N ILE B 542 " --> pdb=" O LEU B 627 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 263 hydrogen bonds defined for protein. 753 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: 1.50 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1630 1.31 - 1.44: 2801 1.44 - 1.57: 5879 1.57 - 1.70: 11 1.70 - 1.83: 82 Bond restraints: 10403 Sorted by residual: bond pdb=" C3B CO8 A 801 " pdb=" C4B CO8 A 801 " ideal model delta sigma weight residual 1.533 1.307 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C4B CO8 A 801 " pdb=" O4B CO8 A 801 " ideal model delta sigma weight residual 1.448 1.603 -0.155 2.00e-02 2.50e+03 5.99e+01 bond pdb=" C5P CO8 A 801 " pdb=" N4P CO8 A 801 " ideal model delta sigma weight residual 1.348 1.472 -0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" C1' ATP B 801 " pdb=" N9 ATP B 801 " ideal model delta sigma weight residual 1.459 1.380 0.079 1.40e-02 5.10e+03 3.22e+01 bond pdb=" C1B CO8 A 801 " pdb=" O4B CO8 A 801 " ideal model delta sigma weight residual 1.419 1.308 0.111 2.00e-02 2.50e+03 3.06e+01 ... (remaining 10398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 13694 3.45 - 6.89: 356 6.89 - 10.34: 30 10.34 - 13.78: 5 13.78 - 17.23: 1 Bond angle restraints: 14086 Sorted by residual: angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 122.64 17.23 1.00e+00 1.00e+00 2.97e+02 angle pdb=" N ILE B 317 " pdb=" CA ILE B 317 " pdb=" C ILE B 317 " ideal model delta sigma weight residual 111.45 100.41 11.04 9.30e-01 1.16e+00 1.41e+02 angle pdb=" N VAL A 167 " pdb=" CA VAL A 167 " pdb=" C VAL A 167 " ideal model delta sigma weight residual 111.91 104.73 7.18 8.90e-01 1.26e+00 6.51e+01 angle pdb=" PA ATP B 801 " pdb=" O3A ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 136.83 129.58 7.25 1.00e+00 1.00e+00 5.25e+01 angle pdb=" N ILE B 317 " pdb=" CA ILE B 317 " pdb=" CB ILE B 317 " ideal model delta sigma weight residual 110.31 120.81 -10.50 1.60e+00 3.91e-01 4.30e+01 ... (remaining 14081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.03: 5982 29.03 - 58.07: 263 58.07 - 87.10: 29 87.10 - 116.14: 1 116.14 - 145.17: 3 Dihedral angle restraints: 6278 sinusoidal: 2594 harmonic: 3684 Sorted by residual: dihedral pdb=" CA GLN B 316 " pdb=" C GLN B 316 " pdb=" N ILE B 317 " pdb=" CA ILE B 317 " ideal model delta harmonic sigma weight residual 180.00 151.56 28.44 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" C TYR B 541 " pdb=" N TYR B 541 " pdb=" CA TYR B 541 " pdb=" CB TYR B 541 " ideal model delta harmonic sigma weight residual -122.60 -110.54 -12.06 0 2.50e+00 1.60e-01 2.33e+01 dihedral pdb=" C ILE A 652 " pdb=" N ILE A 652 " pdb=" CA ILE A 652 " pdb=" CB ILE A 652 " ideal model delta harmonic sigma weight residual -122.00 -133.38 11.38 0 2.50e+00 1.60e-01 2.07e+01 ... (remaining 6275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 1344 0.117 - 0.233: 202 0.233 - 0.350: 20 0.350 - 0.467: 2 0.467 - 0.583: 1 Chirality restraints: 1569 Sorted by residual: chirality pdb=" CB VAL A 102 " pdb=" CA VAL A 102 " pdb=" CG1 VAL A 102 " pdb=" CG2 VAL A 102 " both_signs ideal model delta sigma weight residual False -2.63 -2.05 -0.58 2.00e-01 2.50e+01 8.50e+00 chirality pdb=" CA THR B 632 " pdb=" N THR B 632 " pdb=" C THR B 632 " pdb=" CB THR B 632 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" CA TYR A 559 " pdb=" N TYR A 559 " pdb=" C TYR A 559 " pdb=" CB TYR A 559 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 1566 not shown) Planarity restraints: 1779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 499 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C GLU A 499 " -0.070 2.00e-02 2.50e+03 pdb=" O GLU A 499 " 0.027 2.00e-02 2.50e+03 pdb=" N GLY A 500 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 299 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C HIS B 299 " -0.064 2.00e-02 2.50e+03 pdb=" O HIS B 299 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU B 300 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 102 " 0.018 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C VAL A 102 " -0.060 2.00e-02 2.50e+03 pdb=" O VAL A 102 " 0.022 2.00e-02 2.50e+03 pdb=" N SER A 103 " 0.020 2.00e-02 2.50e+03 ... (remaining 1776 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1073 2.75 - 3.29: 9944 3.29 - 3.83: 15590 3.83 - 4.36: 20981 4.36 - 4.90: 34034 Nonbonded interactions: 81622 Sorted by model distance: nonbonded pdb=" O ASN B 318 " pdb=" ND2 ASN B 318 " model vdw 2.217 3.120 nonbonded pdb=" O VAL B 349 " pdb=" OG1 THR B 353 " model vdw 2.227 3.040 nonbonded pdb=" O ASP A 221 " pdb=" OG1 THR A 225 " model vdw 2.259 3.040 nonbonded pdb=" NH2 ARG B 554 " pdb=" O VAL B 563 " model vdw 2.369 3.120 nonbonded pdb=" O SER A 226 " pdb=" OG SER A 226 " model vdw 2.393 3.040 ... (remaining 81617 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 67 through 722) selection = (chain 'B' and resid 67 through 722) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.010 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.040 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.009 0.226 10403 Z= 0.585 Angle : 1.335 17.226 14086 Z= 0.887 Chirality : 0.085 0.583 1569 Planarity : 0.006 0.048 1779 Dihedral : 16.439 145.170 3906 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.94 % Favored : 89.83 % Rotamer: Outliers : 1.87 % Allowed : 6.18 % Favored : 91.95 % Cbeta Deviations : 0.25 % 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: -5.80 (0.18), residues: 1258 helix: -3.87 (0.13), residues: 788 sheet: -4.41 (0.88), residues: 22 loop : -3.38 (0.24), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 554 TYR 0.024 0.004 TYR B 541 PHE 0.013 0.003 PHE B 162 TRP 0.025 0.003 TRP B 137 HIS 0.007 0.002 HIS B 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00897 / 0.59 (10403) covalent geometry : angle 1.33535 / 0.89 (14086) hydrogen bonds : bond 0.31413 / 20.46 ( 263) hydrogen bonds : angle 10.96189 / 7.54 ( 753) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.386 Fit side-chains REVERT: A 501 MET cc_start: 0.7678 (mtt) cc_final: 0.7426 (mtm) REVERT: A 503 LEU cc_start: 0.7824 (pp) cc_final: 0.7619 (pp) REVERT: B 380 GLU cc_start: 0.7555 (tt0) cc_final: 0.7195 (tm-30) REVERT: B 422 MET cc_start: 0.7730 (ttp) cc_final: 0.7489 (ttp) REVERT: B 566 MET cc_start: 0.5791 (OUTLIER) cc_final: 0.4864 (tpp) outliers start: 20 outliers final: 12 residues processed: 154 average time/residue: 0.1176 time to fit residues: 25.0033 Evaluate side-chains 129 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 243 PRO Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 566 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN B 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.208650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.155677 restraints weight = 10811.914| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.38 r_work: 0.3695 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10403 Z= 0.137 Angle : 0.646 10.031 14086 Z= 0.337 Chirality : 0.041 0.164 1569 Planarity : 0.004 0.043 1779 Dihedral : 10.922 121.389 1510 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.69 % Allowed : 10.39 % Favored : 87.92 % 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: -5.23 (0.19), residues: 1258 helix: -3.35 (0.14), residues: 812 sheet: -5.56 (0.78), residues: 10 loop : -3.29 (0.25), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 554 TYR 0.017 0.001 TYR A 620 PHE 0.009 0.001 PHE B 434 TRP 0.011 0.001 TRP B 137 HIS 0.004 0.001 HIS B 669 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (10403) covalent geometry : angle 0.64644 / 0.34 (14086) hydrogen bonds : bond 0.03772 / 2.47 ( 263) hydrogen bonds : angle 5.38626 / 3.68 ( 753) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 73 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7739 (pm20) REVERT: A 140 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8583 (tt) REVERT: A 318 ASN cc_start: 0.8522 (t0) cc_final: 0.8254 (t0) REVERT: A 501 MET cc_start: 0.7772 (mtt) cc_final: 0.7345 (mtm) REVERT: A 539 MET cc_start: 0.7551 (ttp) cc_final: 0.7318 (ttm) REVERT: B 128 ARG cc_start: 0.7590 (mtp-110) cc_final: 0.6690 (mpt180) REVERT: B 133 GLN cc_start: 0.8242 (tp-100) cc_final: 0.7922 (mm-40) REVERT: B 200 ASP cc_start: 0.8009 (m-30) cc_final: 0.7768 (m-30) REVERT: B 530 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8170 (p) REVERT: B 566 MET cc_start: 0.5724 (OUTLIER) cc_final: 0.4916 (tpp) outliers start: 18 outliers final: 4 residues processed: 131 average time/residue: 0.1268 time to fit residues: 22.5543 Evaluate side-chains 112 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 566 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 64 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.207098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.153646 restraints weight = 10752.842| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.22 r_work: 0.3349 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10403 Z= 0.156 Angle : 0.617 9.962 14086 Z= 0.316 Chirality : 0.041 0.155 1569 Planarity : 0.004 0.038 1779 Dihedral : 10.364 124.157 1491 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.40 % Allowed : 13.01 % Favored : 85.58 % 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: -4.92 (0.19), residues: 1258 helix: -3.03 (0.15), residues: 818 sheet: -5.53 (0.60), residues: 20 loop : -3.25 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 163 TYR 0.021 0.001 TYR B 174 PHE 0.010 0.001 PHE B 434 TRP 0.011 0.001 TRP B 137 HIS 0.003 0.001 HIS A 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (10403) covalent geometry : angle 0.61740 / 0.32 (14086) hydrogen bonds : bond 0.03553 / 2.33 ( 263) hydrogen bonds : angle 4.81935 / 3.29 ( 753) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.421 Fit side-chains REVERT: A 73 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7652 (pm20) REVERT: A 318 ASN cc_start: 0.8713 (t0) cc_final: 0.8478 (t0) REVERT: A 501 MET cc_start: 0.7848 (mtt) cc_final: 0.7480 (mtm) REVERT: B 128 ARG cc_start: 0.7585 (mtp-110) cc_final: 0.6529 (mpt180) REVERT: B 133 GLN cc_start: 0.8385 (tp-100) cc_final: 0.8132 (mm-40) REVERT: B 200 ASP cc_start: 0.8156 (m-30) cc_final: 0.7877 (m-30) REVERT: B 335 MET cc_start: 0.8950 (mtp) cc_final: 0.8712 (ttm) REVERT: B 530 VAL cc_start: 0.8133 (OUTLIER) cc_final: 0.7908 (p) REVERT: B 581 ASP cc_start: 0.7517 (t0) cc_final: 0.7136 (p0) outliers start: 15 outliers final: 3 residues processed: 114 average time/residue: 0.1161 time to fit residues: 18.5299 Evaluate side-chains 102 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 668 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 71 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 0.0670 chunk 17 optimal weight: 4.9990 chunk 83 optimal weight: 0.0270 chunk 73 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.210595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.157278 restraints weight = 10761.745| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.44 r_work: 0.3708 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10403 Z= 0.117 Angle : 0.569 9.355 14086 Z= 0.290 Chirality : 0.040 0.162 1569 Planarity : 0.004 0.035 1779 Dihedral : 9.515 120.203 1484 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.40 % Allowed : 14.98 % Favored : 83.61 % 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: -4.54 (0.20), residues: 1258 helix: -2.72 (0.16), residues: 817 sheet: -5.37 (0.65), residues: 20 loop : -3.14 (0.25), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 80 TYR 0.014 0.001 TYR B 174 PHE 0.008 0.001 PHE A 106 TRP 0.009 0.001 TRP B 137 HIS 0.004 0.001 HIS A 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (10403) covalent geometry : angle 0.56900 / 0.29 (14086) hydrogen bonds : bond 0.02901 / 1.88 ( 263) hydrogen bonds : angle 4.40386 / 3.01 ( 753) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.561 Fit side-chains REVERT: A 73 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: A 133 GLN cc_start: 0.7975 (tp-100) cc_final: 0.7448 (mm-40) REVERT: A 140 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8530 (tt) REVERT: A 318 ASN cc_start: 0.8593 (t0) cc_final: 0.8337 (t0) REVERT: A 501 MET cc_start: 0.7750 (mtt) cc_final: 0.7386 (mtm) REVERT: A 505 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7436 (mt) REVERT: A 539 MET cc_start: 0.7514 (ttp) cc_final: 0.7213 (ttm) REVERT: A 609 GLU cc_start: 0.7997 (tt0) cc_final: 0.7044 (tp30) REVERT: B 128 ARG cc_start: 0.7563 (mtp-110) cc_final: 0.6624 (mpt180) REVERT: B 200 ASP cc_start: 0.7926 (m-30) cc_final: 0.7627 (m-30) REVERT: B 433 HIS cc_start: 0.8336 (t70) cc_final: 0.7951 (t-170) REVERT: B 530 VAL cc_start: 0.8235 (OUTLIER) cc_final: 0.8031 (p) REVERT: B 566 MET cc_start: 0.5751 (tmm) cc_final: 0.4874 (tpp) REVERT: B 596 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7749 (mm-30) REVERT: B 611 GLN cc_start: 0.7598 (mm110) cc_final: 0.7364 (mt0) outliers start: 15 outliers final: 7 residues processed: 117 average time/residue: 0.0909 time to fit residues: 15.1759 Evaluate side-chains 110 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 668 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 11 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 120 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.208805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.154856 restraints weight = 10698.569| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.52 r_work: 0.3677 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10403 Z= 0.147 Angle : 0.586 12.308 14086 Z= 0.296 Chirality : 0.042 0.155 1569 Planarity : 0.004 0.036 1779 Dihedral : 9.374 120.098 1484 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.06 % Allowed : 15.07 % Favored : 82.87 % 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: -4.41 (0.21), residues: 1258 helix: -2.63 (0.16), residues: 821 sheet: -5.35 (0.67), residues: 20 loop : -3.05 (0.26), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 163 TYR 0.018 0.001 TYR B 174 PHE 0.012 0.001 PHE A 71 TRP 0.010 0.001 TRP B 137 HIS 0.003 0.001 HIS A 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (10403) covalent geometry : angle 0.58622 / 0.30 (14086) hydrogen bonds : bond 0.03046 / 1.99 ( 263) hydrogen bonds : angle 4.33724 / 2.96 ( 753) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.347 Fit side-chains REVERT: A 73 GLN cc_start: 0.7946 (mp10) cc_final: 0.7687 (pm20) REVERT: A 98 SER cc_start: 0.8346 (OUTLIER) cc_final: 0.8016 (m) REVERT: A 140 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8634 (tt) REVERT: A 318 ASN cc_start: 0.8599 (t0) cc_final: 0.8334 (t0) REVERT: A 501 MET cc_start: 0.7779 (mtt) cc_final: 0.7415 (mtp) REVERT: A 505 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7472 (mt) REVERT: A 539 MET cc_start: 0.7540 (ttp) cc_final: 0.7248 (ttm) REVERT: A 598 MET cc_start: 0.7719 (mtt) cc_final: 0.7287 (mtp) REVERT: A 609 GLU cc_start: 0.8012 (tt0) cc_final: 0.7150 (tp30) REVERT: B 128 ARG cc_start: 0.7613 (mtp-110) cc_final: 0.6648 (mpt180) REVERT: B 200 ASP cc_start: 0.7980 (m-30) cc_final: 0.7700 (m-30) REVERT: B 433 HIS cc_start: 0.8360 (t70) cc_final: 0.7972 (t-170) REVERT: B 496 ARG cc_start: 0.7867 (tpp-160) cc_final: 0.7659 (tpp-160) REVERT: B 530 VAL cc_start: 0.8218 (OUTLIER) cc_final: 0.7998 (p) REVERT: B 566 MET cc_start: 0.5709 (tmm) cc_final: 0.4829 (tpp) REVERT: B 611 GLN cc_start: 0.7638 (mm110) cc_final: 0.7424 (mt0) outliers start: 22 outliers final: 11 residues processed: 122 average time/residue: 0.0871 time to fit residues: 15.1328 Evaluate side-chains 118 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 668 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 11 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 82 optimal weight: 0.0770 chunk 2 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 8 optimal weight: 0.0980 chunk 39 optimal weight: 0.0970 chunk 120 optimal weight: 6.9990 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.213268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.160568 restraints weight = 10633.563| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 1.75 r_work: 0.3738 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 10403 Z= 0.102 Angle : 0.547 10.156 14086 Z= 0.276 Chirality : 0.040 0.158 1569 Planarity : 0.004 0.037 1779 Dihedral : 8.854 117.737 1484 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.50 % Allowed : 16.29 % Favored : 82.21 % 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: -4.06 (0.21), residues: 1258 helix: -2.36 (0.17), residues: 819 sheet: -5.10 (0.72), residues: 20 loop : -2.91 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 538 TYR 0.010 0.001 TYR B 174 PHE 0.007 0.001 PHE A 106 TRP 0.010 0.001 TRP B 595 HIS 0.004 0.000 HIS A 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 (10403) covalent geometry : angle 0.54653 / 0.28 (14086) hydrogen bonds : bond 0.02575 / 1.67 ( 263) hydrogen bonds : angle 4.03395 / 2.76 ( 753) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.233 Fit side-chains REVERT: A 73 GLN cc_start: 0.8030 (mp10) cc_final: 0.7726 (pm20) REVERT: A 140 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8534 (tt) REVERT: A 318 ASN cc_start: 0.8665 (t0) cc_final: 0.8428 (t0) REVERT: A 501 MET cc_start: 0.7737 (mtt) cc_final: 0.7383 (mtp) REVERT: A 505 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7498 (mt) REVERT: A 537 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7576 (tm130) REVERT: A 539 MET cc_start: 0.7488 (ttp) cc_final: 0.7095 (ttm) REVERT: A 598 MET cc_start: 0.7665 (mtt) cc_final: 0.7190 (mtp) REVERT: A 609 GLU cc_start: 0.8097 (tt0) cc_final: 0.7243 (tp30) REVERT: A 645 GLN cc_start: 0.7854 (tt0) cc_final: 0.7469 (tp40) REVERT: B 128 ARG cc_start: 0.7722 (mtp-110) cc_final: 0.6737 (mpt180) REVERT: B 200 ASP cc_start: 0.8051 (m-30) cc_final: 0.7778 (m-30) REVERT: B 433 HIS cc_start: 0.8428 (t70) cc_final: 0.8027 (t-170) REVERT: B 530 VAL cc_start: 0.8132 (OUTLIER) cc_final: 0.7911 (p) REVERT: B 537 GLN cc_start: 0.7617 (tp-100) cc_final: 0.7109 (tt0) REVERT: B 566 MET cc_start: 0.5730 (tmm) cc_final: 0.4824 (tpp) REVERT: B 611 GLN cc_start: 0.7764 (mm110) cc_final: 0.7562 (mt0) REVERT: B 619 PHE cc_start: 0.8574 (m-80) cc_final: 0.8360 (m-10) outliers start: 16 outliers final: 7 residues processed: 121 average time/residue: 0.0964 time to fit residues: 16.3451 Evaluate side-chains 112 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 531 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.209964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.155973 restraints weight = 10562.755| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.37 r_work: 0.3690 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10403 Z= 0.141 Angle : 0.578 10.254 14086 Z= 0.289 Chirality : 0.041 0.153 1569 Planarity : 0.004 0.040 1779 Dihedral : 8.843 118.019 1484 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.15 % Allowed : 16.29 % Favored : 81.55 % 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: -4.01 (0.21), residues: 1258 helix: -2.32 (0.17), residues: 819 sheet: -5.02 (0.75), residues: 20 loop : -2.90 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 80 TYR 0.018 0.001 TYR B 174 PHE 0.010 0.001 PHE A 333 TRP 0.010 0.001 TRP B 137 HIS 0.003 0.001 HIS A 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (10403) covalent geometry : angle 0.57754 / 0.29 (14086) hydrogen bonds : bond 0.02865 / 1.88 ( 263) hydrogen bonds : angle 4.08944 / 2.79 ( 753) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 140 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8592 (tt) REVERT: A 318 ASN cc_start: 0.8582 (t0) cc_final: 0.8337 (t0) REVERT: A 477 GLU cc_start: 0.6659 (mp0) cc_final: 0.6423 (mp0) REVERT: A 501 MET cc_start: 0.7666 (mtt) cc_final: 0.7297 (mtp) REVERT: A 505 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7437 (mt) REVERT: A 537 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7561 (tm130) REVERT: A 539 MET cc_start: 0.7478 (ttp) cc_final: 0.7173 (ttm) REVERT: A 598 MET cc_start: 0.7667 (mtt) cc_final: 0.7181 (mtp) REVERT: A 609 GLU cc_start: 0.7982 (tt0) cc_final: 0.7068 (tp30) REVERT: A 645 GLN cc_start: 0.7844 (tt0) cc_final: 0.7456 (tp40) REVERT: B 128 ARG cc_start: 0.7620 (mtp-110) cc_final: 0.6689 (mpt180) REVERT: B 433 HIS cc_start: 0.8382 (t70) cc_final: 0.7970 (t-170) REVERT: B 530 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7895 (p) REVERT: B 566 MET cc_start: 0.5617 (tmm) cc_final: 0.4707 (tpp) REVERT: B 611 GLN cc_start: 0.7702 (mm110) cc_final: 0.7494 (mt0) REVERT: B 619 PHE cc_start: 0.8486 (m-80) cc_final: 0.8229 (m-10) outliers start: 23 outliers final: 14 residues processed: 119 average time/residue: 0.0861 time to fit residues: 14.8233 Evaluate side-chains 121 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 668 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 60 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 0.0030 chunk 105 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.212284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.157753 restraints weight = 10626.758| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.42 r_work: 0.3703 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10403 Z= 0.115 Angle : 0.558 9.390 14086 Z= 0.278 Chirality : 0.040 0.157 1569 Planarity : 0.004 0.038 1779 Dihedral : 8.614 116.278 1484 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.25 % Allowed : 16.85 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.83 (0.22), residues: 1258 helix: -2.18 (0.17), residues: 816 sheet: -4.76 (0.84), residues: 20 loop : -2.85 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 80 TYR 0.013 0.001 TYR B 174 PHE 0.011 0.001 PHE A 333 TRP 0.009 0.001 TRP B 137 HIS 0.004 0.001 HIS A 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (10403) covalent geometry : angle 0.55751 / 0.28 (14086) hydrogen bonds : bond 0.02632 / 1.72 ( 263) hydrogen bonds : angle 3.96047 / 2.71 ( 753) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.372 Fit side-chains REVERT: A 98 SER cc_start: 0.8304 (OUTLIER) cc_final: 0.7953 (m) REVERT: A 140 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8544 (tt) REVERT: A 318 ASN cc_start: 0.8571 (t0) cc_final: 0.8322 (t0) REVERT: A 472 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7278 (pp30) REVERT: A 477 GLU cc_start: 0.6662 (mp0) cc_final: 0.6360 (mp0) REVERT: A 496 ARG cc_start: 0.8059 (ttm110) cc_final: 0.7524 (tpp80) REVERT: A 501 MET cc_start: 0.7645 (mtt) cc_final: 0.7308 (mtp) REVERT: A 505 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7354 (mt) REVERT: A 537 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7599 (tm130) REVERT: A 539 MET cc_start: 0.7425 (ttp) cc_final: 0.7046 (ttm) REVERT: A 598 MET cc_start: 0.7600 (mtt) cc_final: 0.7119 (mtp) REVERT: A 609 GLU cc_start: 0.7983 (tt0) cc_final: 0.7070 (tp30) REVERT: A 645 GLN cc_start: 0.7815 (tt0) cc_final: 0.7427 (tp40) REVERT: B 128 ARG cc_start: 0.7648 (mtp-110) cc_final: 0.6715 (mpt180) REVERT: B 433 HIS cc_start: 0.8378 (t70) cc_final: 0.7957 (t-170) REVERT: B 530 VAL cc_start: 0.8032 (OUTLIER) cc_final: 0.7809 (p) REVERT: B 566 MET cc_start: 0.5540 (tmm) cc_final: 0.4637 (tpp) REVERT: B 619 PHE cc_start: 0.8464 (m-80) cc_final: 0.8175 (m-10) outliers start: 24 outliers final: 15 residues processed: 121 average time/residue: 0.0775 time to fit residues: 13.6322 Evaluate side-chains 124 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 668 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 117 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 68 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.0040 chunk 54 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 64 optimal weight: 0.0270 overall best weight: 0.3450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 ASN A 672 GLN B 502 HIS B 537 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.220470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.168762 restraints weight = 10617.756| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 1.74 r_work: 0.3763 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 10403 Z= 0.102 Angle : 0.548 8.984 14086 Z= 0.274 Chirality : 0.040 0.157 1569 Planarity : 0.004 0.039 1779 Dihedral : 8.353 114.805 1484 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.15 % Allowed : 16.85 % Favored : 80.99 % 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: -3.60 (0.22), residues: 1258 helix: -1.97 (0.17), residues: 816 sheet: -4.49 (0.91), residues: 20 loop : -2.82 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 80 TYR 0.011 0.001 TYR B 174 PHE 0.013 0.001 PHE B 540 TRP 0.009 0.001 TRP B 137 HIS 0.004 0.000 HIS A 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.10 (10403) covalent geometry : angle 0.54830 / 0.27 (14086) hydrogen bonds : bond 0.02480 / 1.61 ( 263) hydrogen bonds : angle 3.82504 / 2.62 ( 753) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.355 Fit side-chains REVERT: A 98 SER cc_start: 0.8345 (OUTLIER) cc_final: 0.8019 (m) REVERT: A 140 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8508 (tt) REVERT: A 318 ASN cc_start: 0.8639 (t0) cc_final: 0.8412 (t0) REVERT: A 472 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7269 (pp30) REVERT: A 477 GLU cc_start: 0.6650 (mp0) cc_final: 0.6346 (mp0) REVERT: A 496 ARG cc_start: 0.8014 (ttm110) cc_final: 0.7573 (tpp80) REVERT: A 501 MET cc_start: 0.7699 (mtt) cc_final: 0.7352 (mtp) REVERT: A 505 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7444 (mt) REVERT: A 537 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7643 (tm130) REVERT: A 539 MET cc_start: 0.7437 (ttp) cc_final: 0.7073 (ttm) REVERT: A 598 MET cc_start: 0.7641 (mtt) cc_final: 0.7201 (mtp) REVERT: A 609 GLU cc_start: 0.8080 (tt0) cc_final: 0.7177 (tp30) REVERT: B 128 ARG cc_start: 0.7738 (mtp-110) cc_final: 0.6734 (mpt180) REVERT: B 433 HIS cc_start: 0.8437 (t70) cc_final: 0.8017 (t-170) REVERT: B 537 GLN cc_start: 0.7645 (tp-100) cc_final: 0.7326 (tt0) REVERT: B 566 MET cc_start: 0.5594 (tmm) cc_final: 0.4721 (tpp) REVERT: B 619 PHE cc_start: 0.8531 (m-80) cc_final: 0.8271 (m-80) outliers start: 23 outliers final: 14 residues processed: 123 average time/residue: 0.0937 time to fit residues: 16.8992 Evaluate side-chains 122 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 531 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 103 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 50 optimal weight: 0.0980 chunk 97 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 ASN ** B 502 HIS ** 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 = 0.4475 r_free = 0.4475 target = 0.219143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.167048 restraints weight = 10614.955| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 1.75 r_work: 0.3739 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10403 Z= 0.125 Angle : 0.564 8.993 14086 Z= 0.281 Chirality : 0.041 0.155 1569 Planarity : 0.004 0.039 1779 Dihedral : 8.344 114.318 1484 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.15 % Allowed : 17.13 % Favored : 80.71 % 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: -3.53 (0.22), residues: 1258 helix: -1.93 (0.17), residues: 816 sheet: -4.41 (0.95), residues: 20 loop : -2.80 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 80 TYR 0.015 0.001 TYR B 174 PHE 0.022 0.001 PHE B 540 TRP 0.011 0.001 TRP B 137 HIS 0.004 0.001 HIS B 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.12 (10403) covalent geometry : angle 0.56416 / 0.28 (14086) hydrogen bonds : bond 0.02665 / 1.74 ( 263) hydrogen bonds : angle 3.86026 / 2.65 ( 753) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.285 Fit side-chains REVERT: A 98 SER cc_start: 0.8357 (OUTLIER) cc_final: 0.7999 (m) REVERT: A 140 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8534 (tt) REVERT: A 318 ASN cc_start: 0.8513 (t0) cc_final: 0.8261 (t0) REVERT: A 472 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7291 (pp30) REVERT: A 496 ARG cc_start: 0.7920 (ttm110) cc_final: 0.7559 (tpp80) REVERT: A 501 MET cc_start: 0.7576 (mtt) cc_final: 0.7255 (mtp) REVERT: A 505 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7339 (mt) REVERT: A 537 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7666 (tm130) REVERT: A 539 MET cc_start: 0.7349 (ttp) cc_final: 0.7005 (ttm) REVERT: A 598 MET cc_start: 0.7579 (mtt) cc_final: 0.7121 (mtp) REVERT: A 609 GLU cc_start: 0.7980 (tt0) cc_final: 0.7063 (tp30) REVERT: B 128 ARG cc_start: 0.7614 (mtp-110) cc_final: 0.6731 (mpt180) REVERT: B 433 HIS cc_start: 0.8357 (t70) cc_final: 0.7950 (t-170) REVERT: B 537 GLN cc_start: 0.7613 (tp-100) cc_final: 0.7333 (tt0) REVERT: B 538 ARG cc_start: 0.7796 (ptm160) cc_final: 0.7553 (ptm-80) REVERT: B 566 MET cc_start: 0.5502 (tmm) cc_final: 0.4619 (tpp) outliers start: 23 outliers final: 14 residues processed: 119 average time/residue: 0.0902 time to fit residues: 15.4677 Evaluate side-chains 122 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 668 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 6 optimal weight: 0.0770 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 HIS ** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.212451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.158371 restraints weight = 10598.140| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.15 r_work: 0.3695 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10403 Z= 0.131 Angle : 0.575 9.499 14086 Z= 0.285 Chirality : 0.041 0.154 1569 Planarity : 0.004 0.039 1779 Dihedral : 8.336 113.491 1484 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.97 % Allowed : 17.42 % Favored : 80.62 % 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: -3.57 (0.22), residues: 1258 helix: -1.90 (0.17), residues: 820 sheet: -3.12 (0.87), residues: 32 loop : -3.00 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 80 TYR 0.015 0.001 TYR B 174 PHE 0.020 0.001 PHE B 540 TRP 0.012 0.001 TRP B 137 HIS 0.004 0.001 HIS B 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (10403) covalent geometry : angle 0.57522 / 0.28 (14086) hydrogen bonds : bond 0.02704 / 1.77 ( 263) hydrogen bonds : angle 3.92525 / 2.68 ( 753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2435.67 seconds wall clock time: 42 minutes 27.18 seconds (2547.18 seconds total)