Starting phenix.real_space_refine on Mon Jul 28 10:23:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x0t_32924/07_2025/7x0t_32924.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x0t_32924/07_2025/7x0t_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7x0t_32924/07_2025/7x0t_32924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x0t_32924/07_2025/7x0t_32924.map" model { file = "/net/cci-nas-00/data/ceres_data/7x0t_32924/07_2025/7x0t_32924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x0t_32924/07_2025/7x0t_32924.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.27, per 1000 atoms: 0.71 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: 2.84 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.96 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: 2.26 Time building geometry restraints manager: 2.96 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: 6001 29.03 - 58.07: 273 58.07 - 87.10: 31 87.10 - 116.14: 1 116.14 - 145.17: 3 Dihedral angle restraints: 6309 sinusoidal: 2625 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 6306 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: 5.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 25.700 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 : 16.635 145.170 3937 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.025 0.003 TRP B 137 HIS 0.007 0.002 HIS B 659 PHE 0.013 0.003 PHE B 162 TYR 0.024 0.004 TYR B 541 ARG 0.008 0.001 ARG A 554 Details of bonding type rmsd hydrogen bonds : bond 0.31413 ( 263) hydrogen bonds : angle 10.96189 ( 753) covalent geometry : bond 0.00897 (10403) covalent geometry : angle 1.33535 (14086) *********************** 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 : 1.181 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: 0.4865 (tpp) outliers start: 20 outliers final: 12 residues processed: 154 average time/residue: 0.2680 time to fit residues: 56.6111 Evaluate side-chains 128 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 106 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 64 optimal weight: 0.3980 chunk 51 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 73 optimal weight: 0.0980 chunk 114 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4383 r_free = 0.4383 target = 0.207680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.154617 restraints weight = 10769.506| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.54 r_work: 0.3686 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1487 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= 0.144 Angle : 0.655 10.135 14086 Z= 0.342 Chirality : 0.041 0.164 1569 Planarity : 0.005 0.049 1779 Dihedral : 11.396 122.651 1541 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 1.69 % Allowed : 10.21 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.25 (0.19), residues: 1258 helix: -3.36 (0.14), residues: 813 sheet: -5.59 (0.78), residues: 10 loop : -3.31 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 137 HIS 0.003 0.001 HIS B 502 PHE 0.010 0.001 PHE B 434 TYR 0.018 0.002 TYR B 174 ARG 0.003 0.000 ARG B 554 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 263) hydrogen bonds : angle 5.45563 ( 753) covalent geometry : bond 0.00340 (10403) covalent geometry : angle 0.65483 (14086) *********************** 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 133 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.178 Fit side-chains REVERT: A 73 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7683 (pm20) REVERT: A 140 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8587 (tt) REVERT: A 318 ASN cc_start: 0.8535 (t0) cc_final: 0.8267 (t0) REVERT: A 501 MET cc_start: 0.7772 (mtt) cc_final: 0.7331 (mtm) REVERT: A 539 MET cc_start: 0.7582 (ttp) cc_final: 0.7326 (ttm) REVERT: B 133 GLN cc_start: 0.8275 (tp-100) cc_final: 0.7947 (mm-40) REVERT: B 200 ASP cc_start: 0.8031 (m-30) cc_final: 0.7794 (m-30) REVERT: B 530 VAL cc_start: 0.8401 (OUTLIER) cc_final: 0.8189 (p) REVERT: B 566 MET cc_start: 0.5680 (OUTLIER) cc_final: 0.4880 (tpp) outliers start: 18 outliers final: 4 residues processed: 127 average time/residue: 0.2860 time to fit residues: 49.2870 Evaluate side-chains 105 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 1.766 ------------------------------------------------------------------------------- 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 38 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 97 optimal weight: 0.0980 chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 210 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.205019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.151661 restraints weight = 10888.756| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.13 r_work: 0.3276 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10403 Z= 0.183 Angle : 0.642 10.062 14086 Z= 0.329 Chirality : 0.043 0.155 1569 Planarity : 0.004 0.039 1779 Dihedral : 10.935 121.995 1522 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.59 % Allowed : 13.20 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.01 (0.19), residues: 1258 helix: -3.11 (0.15), residues: 818 sheet: -5.57 (0.60), residues: 20 loop : -3.26 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 137 HIS 0.003 0.001 HIS B 97 PHE 0.011 0.001 PHE B 434 TYR 0.023 0.002 TYR B 174 ARG 0.004 0.000 ARG B 554 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 263) hydrogen bonds : angle 4.98231 ( 753) covalent geometry : bond 0.00447 (10403) covalent geometry : angle 0.64203 (14086) *********************** 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 121 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 1.089 Fit side-chains REVERT: A 73 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: A 98 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.8062 (m) REVERT: A 318 ASN cc_start: 0.8748 (t0) cc_final: 0.8504 (t0) REVERT: A 501 MET cc_start: 0.7865 (mtt) cc_final: 0.7501 (mtm) REVERT: B 133 GLN cc_start: 0.8456 (tp-100) cc_final: 0.8215 (mm-40) REVERT: B 200 ASP cc_start: 0.8160 (m-30) cc_final: 0.7895 (m-30) REVERT: B 210 HIS cc_start: 0.7560 (OUTLIER) cc_final: 0.7288 (m90) REVERT: B 530 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7955 (p) outliers start: 17 outliers final: 5 residues processed: 115 average time/residue: 0.2464 time to fit residues: 39.8684 Evaluate side-chains 106 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 210 HIS 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 50 optimal weight: 10.0000 chunk 1 optimal weight: 0.3980 chunk 119 optimal weight: 2.9990 chunk 10 optimal weight: 0.0070 chunk 57 optimal weight: 8.9990 chunk 11 optimal weight: 0.4980 chunk 86 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS B 586 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.210007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.156819 restraints weight = 10631.071| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.30 r_work: 0.3710 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2057 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= 0.114 Angle : 0.577 9.326 14086 Z= 0.295 Chirality : 0.040 0.163 1569 Planarity : 0.004 0.036 1779 Dihedral : 9.972 115.730 1515 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.31 % Allowed : 15.17 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.20), residues: 1258 helix: -2.80 (0.16), residues: 817 sheet: -5.48 (0.63), residues: 20 loop : -3.15 (0.25), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 137 HIS 0.009 0.001 HIS B 210 PHE 0.008 0.001 PHE B 540 TYR 0.013 0.001 TYR B 174 ARG 0.003 0.000 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.02981 ( 263) hydrogen bonds : angle 4.47755 ( 753) covalent geometry : bond 0.00273 (10403) covalent geometry : angle 0.57702 (14086) *********************** 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 118 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 1.436 Fit side-chains revert: symmetry clash REVERT: A 73 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: A 140 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8544 (tt) REVERT: A 318 ASN cc_start: 0.8598 (t0) cc_final: 0.8347 (t0) REVERT: A 501 MET cc_start: 0.7763 (mtt) cc_final: 0.7393 (mtm) REVERT: A 539 MET cc_start: 0.7559 (ttp) cc_final: 0.7248 (ttm) REVERT: B 128 ARG cc_start: 0.7558 (mtp-110) cc_final: 0.6615 (mpt180) REVERT: B 200 ASP cc_start: 0.7980 (m-30) cc_final: 0.7675 (m-30) REVERT: B 496 ARG cc_start: 0.7813 (tpp-160) cc_final: 0.7607 (tpp-160) REVERT: B 530 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8048 (p) REVERT: B 566 MET cc_start: 0.5649 (tmm) cc_final: 0.4818 (tpp) REVERT: B 581 ASP cc_start: 0.7532 (t0) cc_final: 0.7104 (p0) outliers start: 14 outliers final: 7 residues processed: 112 average time/residue: 0.2571 time to fit residues: 41.6698 Evaluate side-chains 108 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 258 LEU Chi-restraints excluded: chain A residue 400 GLU 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 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 66 optimal weight: 0.0170 chunk 63 optimal weight: 5.9990 chunk 114 optimal weight: 0.0050 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 105 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 107 optimal weight: 0.3980 overall best weight: 0.3032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4431 r_free = 0.4431 target = 0.213214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.160009 restraints weight = 10499.912| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.22 r_work: 0.3737 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2409 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= 0.103 Angle : 0.550 11.721 14086 Z= 0.279 Chirality : 0.040 0.158 1569 Planarity : 0.003 0.036 1779 Dihedral : 9.327 112.509 1515 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.50 % Allowed : 15.17 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.21), residues: 1258 helix: -2.49 (0.17), residues: 818 sheet: -5.27 (0.67), residues: 20 loop : -3.02 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 679 HIS 0.004 0.001 HIS A 621 PHE 0.016 0.001 PHE A 71 TYR 0.011 0.001 TYR B 174 ARG 0.004 0.000 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.02696 ( 263) hydrogen bonds : angle 4.13080 ( 753) covalent geometry : bond 0.00245 (10403) covalent geometry : angle 0.55001 (14086) *********************** 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 131 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.181 Fit side-chains REVERT: A 73 GLN cc_start: 0.7951 (mp10) cc_final: 0.7694 (pm20) REVERT: A 133 GLN cc_start: 0.7876 (tp-100) cc_final: 0.7459 (mm-40) REVERT: A 140 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8436 (tt) REVERT: A 318 ASN cc_start: 0.8577 (t0) cc_final: 0.8322 (t0) REVERT: A 501 MET cc_start: 0.7749 (mtt) cc_final: 0.7397 (mtp) REVERT: A 505 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7450 (mt) REVERT: A 537 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7538 (tm130) REVERT: A 539 MET cc_start: 0.7449 (ttp) cc_final: 0.7062 (ttm) REVERT: A 598 MET cc_start: 0.7673 (mtt) cc_final: 0.7241 (mtp) REVERT: A 609 GLU cc_start: 0.8069 (tt0) cc_final: 0.7193 (tp30) REVERT: B 128 ARG cc_start: 0.7598 (mtp-110) cc_final: 0.6710 (mpt180) REVERT: B 200 ASP cc_start: 0.7867 (m-30) cc_final: 0.7569 (m-30) REVERT: B 433 HIS cc_start: 0.8334 (t70) cc_final: 0.7939 (t-170) REVERT: B 530 VAL cc_start: 0.8166 (OUTLIER) cc_final: 0.7961 (p) REVERT: B 537 GLN cc_start: 0.7306 (tp-100) cc_final: 0.6911 (tt0) REVERT: B 566 MET cc_start: 0.5599 (tmm) cc_final: 0.4734 (tpp) REVERT: B 596 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7764 (mm-30) outliers start: 16 outliers final: 6 residues processed: 124 average time/residue: 0.2361 time to fit residues: 41.6032 Evaluate side-chains 114 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 258 LEU 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 537 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 5.9990 chunk 13 optimal weight: 0.0570 chunk 74 optimal weight: 0.8980 chunk 79 optimal weight: 0.0980 chunk 81 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 105 optimal weight: 0.0980 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4432 r_free = 0.4432 target = 0.213620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.160022 restraints weight = 10588.497| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.97 r_work: 0.3771 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2591 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= 0.104 Angle : 0.547 10.414 14086 Z= 0.276 Chirality : 0.040 0.157 1569 Planarity : 0.003 0.037 1779 Dihedral : 9.017 110.121 1515 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.50 % Allowed : 15.73 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.21), residues: 1258 helix: -2.32 (0.17), residues: 817 sheet: -5.06 (0.70), residues: 20 loop : -2.90 (0.27), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 137 HIS 0.003 0.001 HIS A 621 PHE 0.008 0.001 PHE B 540 TYR 0.011 0.001 TYR B 174 ARG 0.004 0.000 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.02623 ( 263) hydrogen bonds : angle 3.97693 ( 753) covalent geometry : bond 0.00249 (10403) covalent geometry : angle 0.54682 (14086) *********************** 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 127 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 1.172 Fit side-chains REVERT: A 73 GLN cc_start: 0.8034 (mp10) cc_final: 0.7825 (mp10) REVERT: A 140 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8469 (tt) REVERT: A 318 ASN cc_start: 0.8647 (t0) cc_final: 0.8409 (t0) REVERT: A 501 MET cc_start: 0.7792 (mtt) cc_final: 0.7419 (mtp) REVERT: A 505 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7505 (mt) REVERT: A 537 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7580 (tm130) REVERT: A 539 MET cc_start: 0.7499 (ttp) cc_final: 0.7089 (ttm) REVERT: A 598 MET cc_start: 0.7628 (mtt) cc_final: 0.7154 (mtp) REVERT: A 609 GLU cc_start: 0.8157 (tt0) cc_final: 0.7253 (tp30) REVERT: B 128 ARG cc_start: 0.7741 (mtp-110) cc_final: 0.6714 (mpt180) REVERT: B 200 ASP cc_start: 0.8006 (m-30) cc_final: 0.7722 (m-30) REVERT: B 433 HIS cc_start: 0.8422 (t70) cc_final: 0.8006 (t-170) REVERT: B 493 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7556 (mp) REVERT: B 496 ARG cc_start: 0.7928 (tpp-160) cc_final: 0.7453 (tpp-160) REVERT: B 530 VAL cc_start: 0.8084 (OUTLIER) cc_final: 0.7856 (p) REVERT: B 537 GLN cc_start: 0.7541 (tp-100) cc_final: 0.7048 (tt0) REVERT: B 566 MET cc_start: 0.5604 (tmm) cc_final: 0.4735 (tpp) outliers start: 16 outliers final: 8 residues processed: 122 average time/residue: 0.2284 time to fit residues: 39.9998 Evaluate side-chains 116 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 140 ILE 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 537 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 109 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4369 r_free = 0.4369 target = 0.206639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.151644 restraints weight = 10789.901| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.57 r_work: 0.3641 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10403 Z= 0.211 Angle : 0.633 12.441 14086 Z= 0.317 Chirality : 0.044 0.151 1569 Planarity : 0.004 0.039 1779 Dihedral : 9.442 112.540 1515 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.06 % Allowed : 16.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.21), residues: 1258 helix: -2.47 (0.16), residues: 818 sheet: -5.14 (0.69), residues: 20 loop : -3.01 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 137 HIS 0.005 0.001 HIS B 621 PHE 0.013 0.002 PHE A 333 TYR 0.021 0.002 TYR B 174 ARG 0.003 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.03211 ( 263) hydrogen bonds : angle 4.29163 ( 753) covalent geometry : bond 0.00516 (10403) covalent geometry : angle 0.63298 (14086) *********************** 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 131 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.125 Fit side-chains REVERT: A 133 GLN cc_start: 0.7923 (tp-100) cc_final: 0.7454 (mm-40) REVERT: A 140 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8665 (tt) REVERT: A 318 ASN cc_start: 0.8593 (t0) cc_final: 0.8341 (t0) REVERT: A 334 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8587 (mp) REVERT: A 472 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7308 (pp30) REVERT: A 477 GLU cc_start: 0.6705 (mp0) cc_final: 0.6353 (mp0) REVERT: A 501 MET cc_start: 0.7681 (mtt) cc_final: 0.7324 (mtp) REVERT: A 505 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7481 (mt) REVERT: A 537 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7560 (tm130) REVERT: A 539 MET cc_start: 0.7588 (ttp) cc_final: 0.7319 (ttm) REVERT: A 609 GLU cc_start: 0.8104 (tt0) cc_final: 0.7193 (tp30) REVERT: B 433 HIS cc_start: 0.8406 (t70) cc_final: 0.8001 (t-170) REVERT: B 530 VAL cc_start: 0.8210 (OUTLIER) cc_final: 0.7988 (p) REVERT: B 566 MET cc_start: 0.5763 (tmm) cc_final: 0.4903 (tpp) outliers start: 22 outliers final: 11 residues processed: 123 average time/residue: 0.2196 time to fit residues: 38.7871 Evaluate side-chains 123 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 ILE 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 B residue 114 LEU Chi-restraints excluded: chain B residue 219 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 118 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 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 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 HIS ** 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 = 0.4390 r_free = 0.4390 target = 0.208874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.154854 restraints weight = 10686.274| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.44 r_work: 0.3654 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2524 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= 0.149 Angle : 0.590 11.551 14086 Z= 0.296 Chirality : 0.042 0.156 1569 Planarity : 0.004 0.037 1779 Dihedral : 9.224 110.299 1515 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.87 % Allowed : 17.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.21), residues: 1258 helix: -2.36 (0.17), residues: 816 sheet: -5.01 (0.72), residues: 20 loop : -2.95 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 137 HIS 0.004 0.001 HIS A 621 PHE 0.010 0.001 PHE A 333 TYR 0.017 0.001 TYR B 174 ARG 0.004 0.000 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.02856 ( 263) hydrogen bonds : angle 4.14164 ( 753) covalent geometry : bond 0.00363 (10403) covalent geometry : angle 0.59009 (14086) *********************** 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 127 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 1.827 Fit side-chains REVERT: A 140 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8605 (tt) REVERT: A 318 ASN cc_start: 0.8623 (t0) cc_final: 0.8364 (t0) REVERT: A 472 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7265 (pp30) REVERT: A 477 GLU cc_start: 0.6650 (mp0) cc_final: 0.6276 (mp0) REVERT: A 501 MET cc_start: 0.7680 (mtt) cc_final: 0.7312 (mtp) REVERT: A 505 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7486 (mt) REVERT: A 537 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7514 (tm130) REVERT: A 539 MET cc_start: 0.7608 (ttp) cc_final: 0.7304 (ttm) REVERT: A 598 MET cc_start: 0.7661 (mtt) cc_final: 0.7227 (mtp) REVERT: A 609 GLU cc_start: 0.8085 (tt0) cc_final: 0.7144 (tp30) REVERT: B 128 ARG cc_start: 0.7703 (mtp-110) cc_final: 0.6656 (mpt180) REVERT: B 433 HIS cc_start: 0.8411 (t70) cc_final: 0.7998 (t-170) REVERT: B 530 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7874 (p) REVERT: B 566 MET cc_start: 0.5783 (tmm) cc_final: 0.4810 (tpp) outliers start: 20 outliers final: 12 residues processed: 120 average time/residue: 0.2615 time to fit residues: 45.3623 Evaluate side-chains 122 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 ILE 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 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 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 84 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4384 r_free = 0.4384 target = 0.208222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.154068 restraints weight = 10757.515| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.47 r_work: 0.3648 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2562 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= 0.162 Angle : 0.602 11.416 14086 Z= 0.302 Chirality : 0.042 0.155 1569 Planarity : 0.004 0.038 1779 Dihedral : 9.198 110.480 1515 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.87 % Allowed : 17.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.21), residues: 1258 helix: -2.34 (0.17), residues: 816 sheet: -4.99 (0.74), residues: 20 loop : -2.95 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 137 HIS 0.004 0.001 HIS B 621 PHE 0.016 0.001 PHE A 333 TYR 0.018 0.001 TYR B 174 ARG 0.004 0.000 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.02935 ( 263) hydrogen bonds : angle 4.13954 ( 753) covalent geometry : bond 0.00398 (10403) covalent geometry : angle 0.60204 (14086) *********************** 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 130 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.013 Fit side-chains REVERT: A 140 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8645 (tt) REVERT: A 318 ASN cc_start: 0.8635 (t0) cc_final: 0.8371 (t0) REVERT: A 472 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7343 (pp30) REVERT: A 501 MET cc_start: 0.7702 (mtt) cc_final: 0.7354 (mtp) REVERT: A 505 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7509 (mt) REVERT: A 537 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7520 (tm130) REVERT: A 539 MET cc_start: 0.7651 (ttp) cc_final: 0.7347 (ttm) REVERT: A 609 GLU cc_start: 0.8162 (tt0) cc_final: 0.7180 (tp30) REVERT: B 114 LEU cc_start: 0.8472 (tp) cc_final: 0.8267 (tp) REVERT: B 128 ARG cc_start: 0.7693 (mtp-110) cc_final: 0.6668 (mpt180) REVERT: B 433 HIS cc_start: 0.8439 (t70) cc_final: 0.8043 (t-170) REVERT: B 530 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7868 (p) REVERT: B 566 MET cc_start: 0.5788 (tmm) cc_final: 0.4906 (tpp) outliers start: 20 outliers final: 12 residues processed: 122 average time/residue: 0.2344 time to fit residues: 40.7464 Evaluate side-chains 125 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 219 LEU 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 B residue 87 LEU Chi-restraints excluded: chain B residue 219 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 117 optimal weight: 0.3980 chunk 31 optimal weight: 0.0570 chunk 34 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 98 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4416 r_free = 0.4416 target = 0.211869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.157829 restraints weight = 10564.793| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.43 r_work: 0.3685 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10403 Z= 0.115 Angle : 0.572 11.743 14086 Z= 0.285 Chirality : 0.040 0.159 1569 Planarity : 0.004 0.037 1779 Dihedral : 8.855 106.826 1515 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.69 % Allowed : 17.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.22), residues: 1258 helix: -2.15 (0.17), residues: 816 sheet: -4.69 (0.85), residues: 20 loop : -2.86 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 595 HIS 0.004 0.001 HIS A 621 PHE 0.012 0.001 PHE A 333 TYR 0.012 0.001 TYR B 174 ARG 0.004 0.000 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.02612 ( 263) hydrogen bonds : angle 3.94783 ( 753) covalent geometry : bond 0.00281 (10403) covalent geometry : angle 0.57193 (14086) ********************** 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 122 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 1.063 Fit side-chains REVERT: A 140 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8498 (tt) REVERT: A 318 ASN cc_start: 0.8584 (t0) cc_final: 0.8346 (t0) REVERT: A 472 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7319 (pp30) REVERT: A 496 ARG cc_start: 0.8131 (ttm110) cc_final: 0.7648 (tpp80) REVERT: A 501 MET cc_start: 0.7627 (mtt) cc_final: 0.7267 (mtp) REVERT: A 537 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7624 (tm130) REVERT: A 539 MET cc_start: 0.7547 (ttp) cc_final: 0.7212 (ttm) REVERT: A 598 MET cc_start: 0.7696 (mtt) cc_final: 0.7224 (mtp) REVERT: A 609 GLU cc_start: 0.8122 (tt0) cc_final: 0.7117 (tp30) REVERT: B 128 ARG cc_start: 0.7707 (mtp-110) cc_final: 0.6701 (mpt180) REVERT: B 433 HIS cc_start: 0.8439 (t70) cc_final: 0.8044 (t-170) REVERT: B 530 VAL cc_start: 0.7995 (OUTLIER) cc_final: 0.7793 (p) REVERT: B 566 MET cc_start: 0.5718 (tmm) cc_final: 0.4793 (tpp) outliers start: 18 outliers final: 12 residues processed: 114 average time/residue: 0.2212 time to fit residues: 36.4364 Evaluate side-chains 117 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 472 GLN 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 B residue 87 LEU Chi-restraints excluded: chain B residue 219 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 51 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 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 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 GLN ** 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 = 0.4397 r_free = 0.4397 target = 0.209804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.156072 restraints weight = 10507.526| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.45 r_work: 0.3679 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2725 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= 0.148 Angle : 0.600 10.831 14086 Z= 0.297 Chirality : 0.042 0.157 1569 Planarity : 0.004 0.037 1779 Dihedral : 8.899 107.343 1515 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.69 % Allowed : 17.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.21), residues: 1258 helix: -2.15 (0.17), residues: 814 sheet: -4.71 (0.85), residues: 20 loop : -2.88 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 137 HIS 0.004 0.001 HIS B 621 PHE 0.013 0.001 PHE A 333 TYR 0.017 0.001 TYR B 174 ARG 0.004 0.000 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.02794 ( 263) hydrogen bonds : angle 4.00420 ( 753) covalent geometry : bond 0.00365 (10403) covalent geometry : angle 0.60025 (14086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5364.41 seconds wall clock time: 94 minutes 40.00 seconds (5680.00 seconds total)