Starting phenix.real_space_refine on Thu Jul 2 22:49:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hqp_52346/07_2026/9hqp_52346.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hqp_52346/07_2026/9hqp_52346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hqp_52346/07_2026/9hqp_52346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hqp_52346/07_2026/9hqp_52346.map" model { file = "/net/cci-nas-00/data/ceres_data/9hqp_52346/07_2026/9hqp_52346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hqp_52346/07_2026/9hqp_52346.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 73 5.16 5 C 6894 2.51 5 N 1642 2.21 5 O 1785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 10396 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5268 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 28, 'TRANS': 615} Chain breaks: 8 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 5126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5126 Classifications: {'peptide': 637} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 28, 'TRANS': 608} Chain breaks: 8 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 2.46, per 1000 atoms: 0.24 Number of scatterers: 10396 At special positions: 0 Unit cell: (129.965, 76.45, 109.115, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 73 16.00 O 1785 8.00 N 1642 7.00 C 6894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 397.1 milliseconds 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2434 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 61.7% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 90 through 106 removed outlier: 3.691A pdb=" N GLN A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU A 105 " --> pdb=" O TYR A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 Processing helix chain 'A' and resid 206 through 220 removed outlier: 4.505A pdb=" N SER A 210 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.788A pdb=" N SER A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 272 removed outlier: 3.939A pdb=" N GLU A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 309 removed outlier: 7.559A pdb=" N GLU A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N LYS A 295 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE A 296 " --> pdb=" O TYR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 327 Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.525A pdb=" N ILE A 363 " --> pdb=" O ARG A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 375 through 378 Processing helix chain 'A' and resid 379 through 408 removed outlier: 3.893A pdb=" N LEU A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 489 removed outlier: 3.704A pdb=" N ILE A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 473 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 537 removed outlier: 3.976A pdb=" N SER A 510 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 533 " --> pdb=" O GLU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 572 removed outlier: 4.028A pdb=" N LEU A 557 " --> pdb=" O MET A 553 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 565 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 614 Processing helix chain 'A' and resid 614 through 639 removed outlier: 3.775A pdb=" N ASN A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 656 Processing helix chain 'A' and resid 664 through 680 Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.533A pdb=" N ASN A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 747 removed outlier: 3.654A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 759 Processing helix chain 'A' and resid 825 through 854 Processing helix chain 'B' and resid 90 through 106 removed outlier: 3.772A pdb=" N GLN B 94 " --> pdb=" O THR B 90 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 Processing helix chain 'B' and resid 206 through 220 removed outlier: 4.526A pdb=" N SER B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 275 through 279 removed outlier: 4.008A pdb=" N ILE B 279 " --> pdb=" O PRO B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 removed outlier: 3.821A pdb=" N TYR B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B 293 " --> pdb=" O ARG B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 303 Processing helix chain 'B' and resid 304 through 309 Processing helix chain 'B' and resid 309 through 327 removed outlier: 4.177A pdb=" N ALA B 313 " --> pdb=" O MET B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 332 removed outlier: 4.207A pdb=" N CYS B 331 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR B 332 " --> pdb=" O ASP B 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 328 through 332' Processing helix chain 'B' and resid 360 through 363 removed outlier: 3.529A pdb=" N ILE B 363 " --> pdb=" O ARG B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 371 through 376 Processing helix chain 'B' and resid 377 through 408 removed outlier: 4.183A pdb=" N ILE B 381 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLU B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 488 removed outlier: 3.673A pdb=" N ILE B 464 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 487 " --> pdb=" O ILE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 537 removed outlier: 3.859A pdb=" N SER B 510 " --> pdb=" O GLN B 506 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 533 " --> pdb=" O GLU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 572 removed outlier: 3.990A pdb=" N LEU B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER B 565 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 614 Processing helix chain 'B' and resid 614 through 639 removed outlier: 3.981A pdb=" N ASN B 621 " --> pdb=" O ALA B 617 " (cutoff:3.500A) Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 656 Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.693A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 747 removed outlier: 3.656A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 760 removed outlier: 3.577A pdb=" N TYR B 757 " --> pdb=" O ARG B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 854 removed outlier: 3.585A pdb=" N TRP B 829 " --> pdb=" O ASN B 825 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 128 removed outlier: 3.633A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 222 removed outlier: 3.865A pdb=" N LYS A 230 " --> pdb=" O TYR A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 782 through 783 removed outlier: 3.601A pdb=" N SER A 782 " --> pdb=" O TYR A 809 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 126 through 128 removed outlier: 3.532A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 221 through 222 removed outlier: 3.550A pdb=" N LYS B 230 " --> pdb=" O TYR B 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 782 through 783 removed outlier: 3.590A pdb=" N SER B 782 " --> pdb=" O TYR B 809 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1632 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: 1.59 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3099 1.34 - 1.46: 2689 1.46 - 1.58: 4787 1.58 - 1.70: 0 1.70 - 1.81: 114 Bond restraints: 10689 Sorted by residual: bond pdb=" CG PRO A 763 " pdb=" CD PRO A 763 " ideal model delta sigma weight residual 1.503 1.452 0.051 3.40e-02 8.65e+02 2.29e+00 bond pdb=" CA ILE B 346 " pdb=" CB ILE B 346 " ideal model delta sigma weight residual 1.527 1.539 -0.012 1.31e-02 5.83e+03 8.44e-01 bond pdb=" CA PRO A 598 " pdb=" C PRO A 598 " ideal model delta sigma weight residual 1.528 1.517 0.011 1.20e-02 6.94e+03 7.93e-01 bond pdb=" N PRO A 763 " pdb=" CA PRO A 763 " ideal model delta sigma weight residual 1.465 1.482 -0.017 2.03e-02 2.43e+03 7.21e-01 bond pdb=" N PRO B 284 " pdb=" CA PRO B 284 " ideal model delta sigma weight residual 1.479 1.465 0.014 1.71e-02 3.42e+03 6.81e-01 ... (remaining 10684 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 14410 2.79 - 5.58: 92 5.58 - 8.36: 19 8.36 - 11.15: 4 11.15 - 13.94: 1 Bond angle restraints: 14526 Sorted by residual: angle pdb=" CA PRO A 763 " pdb=" N PRO A 763 " pdb=" CD PRO A 763 " ideal model delta sigma weight residual 112.00 103.75 8.25 1.40e+00 5.10e-01 3.47e+01 angle pdb=" CA PRO A 763 " pdb=" CB PRO A 763 " pdb=" CG PRO A 763 " ideal model delta sigma weight residual 104.50 94.64 9.86 1.90e+00 2.77e-01 2.69e+01 angle pdb=" N PRO A 763 " pdb=" CD PRO A 763 " pdb=" CG PRO A 763 " ideal model delta sigma weight residual 103.20 95.55 7.65 1.50e+00 4.44e-01 2.60e+01 angle pdb=" CB PRO A 763 " pdb=" CG PRO A 763 " pdb=" CD PRO A 763 " ideal model delta sigma weight residual 106.10 92.16 13.94 3.20e+00 9.77e-02 1.90e+01 angle pdb=" N PHE A 246 " pdb=" CA PHE A 246 " pdb=" C PHE A 246 " ideal model delta sigma weight residual 108.13 111.77 -3.64 9.00e-01 1.23e+00 1.63e+01 ... (remaining 14521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5609 17.86 - 35.71: 496 35.71 - 53.57: 82 53.57 - 71.42: 20 71.42 - 89.28: 9 Dihedral angle restraints: 6216 sinusoidal: 2434 harmonic: 3782 Sorted by residual: dihedral pdb=" CB CYS B 349 " pdb=" SG CYS B 349 " pdb=" SG CYS B 807 " pdb=" CB CYS B 807 " ideal model delta sinusoidal sigma weight residual 93.00 21.66 71.34 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CB CYS A 349 " pdb=" SG CYS A 349 " pdb=" SG CYS A 807 " pdb=" CB CYS A 807 " ideal model delta sinusoidal sigma weight residual 93.00 22.17 70.83 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CA MET A 309 " pdb=" C MET A 309 " pdb=" N LEU A 310 " pdb=" CA LEU A 310 " ideal model delta harmonic sigma weight residual 180.00 151.84 28.16 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 6213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 918 0.030 - 0.060: 450 0.060 - 0.089: 171 0.089 - 0.119: 56 0.119 - 0.149: 17 Chirality restraints: 1612 Sorted by residual: chirality pdb=" CA PHE B 482 " pdb=" N PHE B 482 " pdb=" C PHE B 482 " pdb=" CB PHE B 482 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CB VAL B 678 " pdb=" CA VAL B 678 " pdb=" CG1 VAL B 678 " pdb=" CG2 VAL B 678 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA TYR B 847 " pdb=" N TYR B 847 " pdb=" C TYR B 847 " pdb=" CB TYR B 847 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 1609 not shown) Planarity restraints: 1781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 818 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO B 819 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 819 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 819 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 763 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO A 764 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 764 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 764 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 715 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO A 716 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 716 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 716 " -0.027 5.00e-02 4.00e+02 ... (remaining 1778 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1219 2.75 - 3.29: 11028 3.29 - 3.82: 17225 3.82 - 4.36: 19741 4.36 - 4.90: 33741 Nonbonded interactions: 82954 Sorted by model distance: nonbonded pdb=" O PHE B 374 " pdb=" OG1 THR B 379 " model vdw 2.210 3.040 nonbonded pdb=" ND2 ASN B 814 " pdb=" O LYS B 823 " model vdw 2.229 3.120 nonbonded pdb=" O PHE A 485 " pdb=" OG1 THR A 488 " model vdw 2.245 3.040 nonbonded pdb=" ND2 ASN A 814 " pdb=" O LYS A 823 " model vdw 2.280 3.120 nonbonded pdb=" O ILE B 744 " pdb=" OG SER B 748 " model vdw 2.284 3.040 ... (remaining 82949 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 58 through 76 or resid 89 through 91 or (resid 92 through \ 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or (resi \ d 95 through 98 and (name N or name CA or name C or name O or name CB )) or resi \ d 99 through 144 or (resid 145 and (name N or name CA or name C or name O or nam \ e CB )) or resid 146 through 218 or (resid 219 and (name N or name CA or name C \ or name O or name CB )) or resid 220 or (resid 221 and (name N or name CA or nam \ e C or name O or name CB )) or resid 222 through 223 or (resid 224 through 228 a \ nd (name N or name CA or name C or name O or name CB )) or resid 229 through 233 \ or (resid 234 and (name N or name CA or name C or name O or name CB )) or resid \ 235 through 242 or (resid 243 through 245 and (name N or name CA or name C or n \ ame O or name CB )) or resid 246 through 249 or (resid 250 and (name N or name C \ A or name C or name O or name CB )) or resid 251 through 265 or (resid 266 and ( \ name N or name CA or name C or name O or name CB )) or resid 267 through 270 or \ (resid 271 through 272 and (name N or name CA or name C or name O or name CB )) \ or resid 273 through 276 or (resid 277 and (name N or name CA or name C or name \ O or name CB )) or resid 278 through 353 or (resid 354 and (name N or name CA or \ name C or name O or name CB )) or resid 355 through 398 or (resid 399 and (name \ N or name CA or name C or name O or name CB )) or resid 400 through 404 or (res \ id 405 and (name N or name CA or name C or name O or name CB )) or resid 406 thr \ ough 488 or resid 501 through 543 or (resid 544 and (name N or name CA or name C \ or name O or name CB )) or resid 545 through 589 or (resid 590 and (name N or n \ ame CA or name C or name O or name CB )) or resid 591 through 643 or (resid 644 \ through 645 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 6 through 719 or (resid 720 and (name N or name CA or name C or name O or name C \ B )) or resid 721 through 1301)) selection = (chain 'B' and ((resid 58 and (name N or name CA or name C or name O or name CB \ )) or resid 59 through 65 or (resid 66 and (name N or name CA or name C or name \ O or name CB )) or resid 67 or (resid 68 through 69 and (name N or name CA or na \ me C or name O or name CB )) or resid 70 through 289 or (resid 290 and (name N o \ r name CA or name C or name O or name CB )) or resid 291 through 368 or (resid 3 \ 69 and (name N or name CA or name C or name O or name CB )) or resid 370 through \ 1301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.350 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10695 Z= 0.138 Angle : 0.663 13.938 14538 Z= 0.352 Chirality : 0.042 0.149 1612 Planarity : 0.005 0.054 1781 Dihedral : 14.237 89.277 3764 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.54 (0.24), residues: 1245 helix: 0.24 (0.20), residues: 722 sheet: -3.00 (1.16), residues: 20 loop : -2.92 (0.24), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 478 TYR 0.020 0.001 TYR A 757 PHE 0.021 0.001 PHE A 393 TRP 0.024 0.002 TRP A 619 HIS 0.004 0.001 HIS B 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (10689) covalent geometry : angle 0.66310 / 0.35 (14526) SS BOND : bond 0.00136 / 0.07 ( 6) SS BOND : angle 0.88783 / 0.50 ( 12) hydrogen bonds : bond 0.14667 / 9.44 ( 550) hydrogen bonds : angle 6.99887 / 4.89 ( 1632) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.388 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.0824 time to fit residues: 19.8504 Evaluate side-chains 132 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.0870 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.0870 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN A 696 ASN B 401 GLN ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.264647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.234635 restraints weight = 13670.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.235539 restraints weight = 10997.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.237890 restraints weight = 9142.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.237927 restraints weight = 6709.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.238697 restraints weight = 6500.874| |-----------------------------------------------------------------------------| r_work (final): 0.4785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10695 Z= 0.127 Angle : 0.597 12.318 14538 Z= 0.310 Chirality : 0.042 0.155 1612 Planarity : 0.005 0.059 1781 Dihedral : 4.613 26.864 1396 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.81 % Allowed : 10.22 % Favored : 88.97 % 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: -1.39 (0.24), residues: 1245 helix: 0.36 (0.20), residues: 732 sheet: -2.99 (1.15), residues: 20 loop : -2.91 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 478 TYR 0.029 0.001 TYR A 828 PHE 0.043 0.002 PHE B 852 TRP 0.011 0.001 TRP A 619 HIS 0.007 0.001 HIS B 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (10689) covalent geometry : angle 0.59694 / 0.31 (14526) SS BOND : bond 0.00149 / 0.09 ( 6) SS BOND : angle 0.80214 / 0.47 ( 12) hydrogen bonds : bond 0.04385 / 2.85 ( 550) hydrogen bonds : angle 5.23555 / 3.64 ( 1632) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 146 average time/residue: 0.0881 time to fit residues: 19.0651 Evaluate side-chains 134 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 697 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 12 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 401 GLN ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.258109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.227844 restraints weight = 13748.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.229667 restraints weight = 11946.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.230627 restraints weight = 10928.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.231356 restraints weight = 7448.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.232104 restraints weight = 6744.907| |-----------------------------------------------------------------------------| r_work (final): 0.4729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10695 Z= 0.181 Angle : 0.628 10.652 14538 Z= 0.330 Chirality : 0.044 0.164 1612 Planarity : 0.005 0.058 1781 Dihedral : 4.815 31.894 1396 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 1.27 % Allowed : 13.83 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.23), residues: 1245 helix: 0.22 (0.19), residues: 733 sheet: None (None), residues: 0 loop : -2.97 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 753 TYR 0.023 0.002 TYR A 306 PHE 0.043 0.002 PHE A 852 TRP 0.013 0.002 TRP B 333 HIS 0.011 0.001 HIS B 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (10689) covalent geometry : angle 0.62753 / 0.33 (14526) SS BOND : bond 0.00242 / 0.14 ( 6) SS BOND : angle 1.29643 / 0.73 ( 12) hydrogen bonds : bond 0.04589 / 2.96 ( 550) hydrogen bonds : angle 5.30196 / 3.68 ( 1632) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 373 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7647 (mt) REVERT: A 573 PHE cc_start: 0.6407 (p90) cc_final: 0.5785 (p90) REVERT: B 478 ARG cc_start: 0.3514 (OUTLIER) cc_final: 0.3047 (ptp-170) outliers start: 14 outliers final: 8 residues processed: 146 average time/residue: 0.0881 time to fit residues: 19.3292 Evaluate side-chains 142 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain B residue 478 ARG Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 697 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 401 GLN ** B 674 GLN ** 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 = 0.4963 r_free = 0.4963 target = 0.259551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.228538 restraints weight = 14241.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.229116 restraints weight = 11640.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.231032 restraints weight = 9946.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.231276 restraints weight = 6722.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.231974 restraints weight = 6502.361| |-----------------------------------------------------------------------------| r_work (final): 0.4724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10695 Z= 0.141 Angle : 0.594 13.072 14538 Z= 0.308 Chirality : 0.042 0.160 1612 Planarity : 0.005 0.057 1781 Dihedral : 4.651 31.403 1396 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.08 % Allowed : 16.00 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.23), residues: 1245 helix: 0.24 (0.19), residues: 738 sheet: -2.70 (1.22), residues: 20 loop : -3.02 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 96 TYR 0.017 0.001 TYR B 305 PHE 0.049 0.002 PHE A 852 TRP 0.014 0.001 TRP B 333 HIS 0.011 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (10689) covalent geometry : angle 0.59364 / 0.31 (14526) SS BOND : bond 0.00175 / 0.10 ( 6) SS BOND : angle 0.79811 / 0.45 ( 12) hydrogen bonds : bond 0.04226 / 2.74 ( 550) hydrogen bonds : angle 5.14139 / 3.56 ( 1632) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.388 Fit side-chains REVERT: A 373 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7637 (mt) REVERT: A 393 PHE cc_start: 0.4075 (OUTLIER) cc_final: 0.3270 (p90) outliers start: 23 outliers final: 12 residues processed: 155 average time/residue: 0.0892 time to fit residues: 20.5356 Evaluate side-chains 144 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 757 TYR Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 90 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 70 optimal weight: 8.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** 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 = 0.4939 r_free = 0.4939 target = 0.255937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.225685 restraints weight = 13743.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.230033 restraints weight = 12619.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.231232 restraints weight = 7910.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.230909 restraints weight = 5924.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.231115 restraints weight = 6025.584| |-----------------------------------------------------------------------------| r_work (final): 0.4719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10695 Z= 0.191 Angle : 0.650 12.899 14538 Z= 0.336 Chirality : 0.044 0.187 1612 Planarity : 0.005 0.058 1781 Dihedral : 4.825 31.690 1396 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.35 % Allowed : 18.17 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.23), residues: 1245 helix: 0.16 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -3.07 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 96 TYR 0.023 0.002 TYR A 306 PHE 0.047 0.002 PHE A 852 TRP 0.014 0.002 TRP B 333 HIS 0.012 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (10689) covalent geometry : angle 0.64949 / 0.34 (14526) SS BOND : bond 0.00389 / 0.26 ( 6) SS BOND : angle 1.07563 / 0.61 ( 12) hydrogen bonds : bond 0.04499 / 2.91 ( 550) hydrogen bonds : angle 5.28705 / 3.66 ( 1632) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.380 Fit side-chains REVERT: A 373 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7668 (mt) REVERT: A 393 PHE cc_start: 0.4458 (OUTLIER) cc_final: 0.3408 (p90) REVERT: A 573 PHE cc_start: 0.6488 (p90) cc_final: 0.5799 (p90) REVERT: B 309 MET cc_start: 0.6745 (OUTLIER) cc_final: 0.6544 (ppp) outliers start: 26 outliers final: 17 residues processed: 144 average time/residue: 0.0863 time to fit residues: 18.6856 Evaluate side-chains 144 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 757 TYR Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 11 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN ** B 674 GLN ** 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 = 0.4941 r_free = 0.4941 target = 0.257054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.225539 restraints weight = 14351.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.228687 restraints weight = 11843.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.229761 restraints weight = 9109.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.230020 restraints weight = 6335.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.230517 restraints weight = 6111.122| |-----------------------------------------------------------------------------| r_work (final): 0.4708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10695 Z= 0.160 Angle : 0.632 13.399 14538 Z= 0.326 Chirality : 0.043 0.172 1612 Planarity : 0.005 0.060 1781 Dihedral : 4.768 31.586 1396 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.89 % Allowed : 20.80 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.23), residues: 1245 helix: 0.20 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -3.06 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 478 TYR 0.019 0.001 TYR B 305 PHE 0.051 0.002 PHE A 852 TRP 0.010 0.001 TRP A 829 HIS 0.014 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (10689) covalent geometry : angle 0.63189 / 0.33 (14526) SS BOND : bond 0.00220 / 0.13 ( 6) SS BOND : angle 1.00740 / 0.53 ( 12) hydrogen bonds : bond 0.04339 / 2.81 ( 550) hydrogen bonds : angle 5.23746 / 3.63 ( 1632) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.285 Fit side-chains REVERT: A 373 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7663 (mt) REVERT: A 386 MET cc_start: 0.4252 (mmt) cc_final: 0.3880 (tpp) REVERT: A 393 PHE cc_start: 0.4539 (OUTLIER) cc_final: 0.3541 (p90) outliers start: 32 outliers final: 19 residues processed: 156 average time/residue: 0.0856 time to fit residues: 20.2325 Evaluate side-chains 140 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 757 TYR Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 5 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN ** B 674 GLN ** 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 = 0.4933 r_free = 0.4933 target = 0.256621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.224455 restraints weight = 14375.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.223982 restraints weight = 11821.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.226475 restraints weight = 10450.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.227031 restraints weight = 7238.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.227254 restraints weight = 7240.679| |-----------------------------------------------------------------------------| r_work (final): 0.4712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10695 Z= 0.151 Angle : 0.647 13.723 14538 Z= 0.330 Chirality : 0.043 0.174 1612 Planarity : 0.005 0.068 1781 Dihedral : 4.739 31.275 1396 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.89 % Allowed : 21.34 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.23), residues: 1245 helix: 0.22 (0.19), residues: 738 sheet: -2.93 (2.06), residues: 10 loop : -3.12 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 478 TYR 0.027 0.001 TYR B 528 PHE 0.050 0.002 PHE A 852 TRP 0.016 0.001 TRP B 333 HIS 0.021 0.002 HIS B 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (10689) covalent geometry : angle 0.64645 / 0.33 (14526) SS BOND : bond 0.00211 / 0.14 ( 6) SS BOND : angle 0.88105 / 0.50 ( 12) hydrogen bonds : bond 0.04254 / 2.76 ( 550) hydrogen bonds : angle 5.17782 / 3.59 ( 1632) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.430 Fit side-chains REVERT: A 373 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7606 (mt) REVERT: A 393 PHE cc_start: 0.4525 (OUTLIER) cc_final: 0.3341 (p90) REVERT: A 478 ARG cc_start: 0.4622 (mtt180) cc_final: 0.4388 (ptp-170) REVERT: A 590 LYS cc_start: 0.7992 (tptt) cc_final: 0.6955 (mptt) REVERT: B 142 MET cc_start: 0.6272 (mmm) cc_final: 0.5906 (mmm) outliers start: 32 outliers final: 21 residues processed: 147 average time/residue: 0.0812 time to fit residues: 18.1087 Evaluate side-chains 142 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 757 TYR Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 11 optimal weight: 0.0670 chunk 77 optimal weight: 0.0070 chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN ** B 674 GLN ** 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 = 0.4968 r_free = 0.4968 target = 0.260325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.229607 restraints weight = 14334.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.231329 restraints weight = 12204.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.232679 restraints weight = 9962.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.233179 restraints weight = 6960.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.233383 restraints weight = 6775.283| |-----------------------------------------------------------------------------| r_work (final): 0.4775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10695 Z= 0.128 Angle : 0.635 14.288 14538 Z= 0.317 Chirality : 0.042 0.161 1612 Planarity : 0.005 0.064 1781 Dihedral : 4.557 29.534 1396 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.08 % Allowed : 23.06 % Favored : 74.86 % 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: -1.48 (0.23), residues: 1245 helix: 0.32 (0.19), residues: 741 sheet: -3.05 (2.04), residues: 10 loop : -3.07 (0.24), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 478 TYR 0.045 0.001 TYR B 528 PHE 0.051 0.001 PHE B 852 TRP 0.013 0.001 TRP B 333 HIS 0.014 0.001 HIS B 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (10689) covalent geometry : angle 0.63517 / 0.32 (14526) SS BOND : bond 0.00122 / 0.07 ( 6) SS BOND : angle 0.65207 / 0.37 ( 12) hydrogen bonds : bond 0.04031 / 2.64 ( 550) hydrogen bonds : angle 5.01943 / 3.49 ( 1632) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.435 Fit side-chains REVERT: A 373 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7642 (mt) REVERT: A 393 PHE cc_start: 0.4126 (OUTLIER) cc_final: 0.3104 (p90) REVERT: A 478 ARG cc_start: 0.4472 (mtt180) cc_final: 0.4237 (ptp-170) REVERT: A 506 GLN cc_start: 0.6308 (OUTLIER) cc_final: 0.4419 (pm20) REVERT: A 678 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8316 (p) REVERT: B 142 MET cc_start: 0.6377 (mmm) cc_final: 0.6071 (mmm) REVERT: B 748 SER cc_start: 0.8494 (p) cc_final: 0.8092 (t) outliers start: 23 outliers final: 15 residues processed: 149 average time/residue: 0.0756 time to fit residues: 17.2908 Evaluate side-chains 135 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 757 TYR Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 4 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 122 optimal weight: 0.0770 chunk 53 optimal weight: 0.5980 chunk 94 optimal weight: 10.0000 chunk 39 optimal weight: 0.0040 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 overall best weight: 0.4750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN ** B 674 GLN ** 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 = 0.4963 r_free = 0.4963 target = 0.260138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.229000 restraints weight = 14407.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.229575 restraints weight = 11510.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.231433 restraints weight = 10366.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.231872 restraints weight = 6711.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.232412 restraints weight = 6431.121| |-----------------------------------------------------------------------------| r_work (final): 0.4758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10695 Z= 0.127 Angle : 0.631 13.975 14538 Z= 0.317 Chirality : 0.042 0.165 1612 Planarity : 0.005 0.062 1781 Dihedral : 4.521 28.218 1396 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.81 % Allowed : 22.97 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.24), residues: 1245 helix: 0.45 (0.19), residues: 737 sheet: -3.07 (2.02), residues: 10 loop : -3.01 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 478 TYR 0.022 0.001 TYR B 138 PHE 0.051 0.002 PHE B 852 TRP 0.024 0.001 TRP B 333 HIS 0.014 0.001 HIS B 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (10689) covalent geometry : angle 0.63065 / 0.32 (14526) SS BOND : bond 0.00105 / 0.07 ( 6) SS BOND : angle 0.62721 / 0.39 ( 12) hydrogen bonds : bond 0.03977 / 2.60 ( 550) hydrogen bonds : angle 4.98572 / 3.46 ( 1632) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.380 Fit side-chains REVERT: A 373 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7656 (mt) REVERT: A 393 PHE cc_start: 0.4109 (OUTLIER) cc_final: 0.3129 (p90) REVERT: A 506 GLN cc_start: 0.6209 (OUTLIER) cc_final: 0.4441 (pm20) REVERT: B 142 MET cc_start: 0.6313 (mmm) cc_final: 0.6080 (mmm) REVERT: B 748 SER cc_start: 0.8431 (p) cc_final: 0.8047 (t) outliers start: 20 outliers final: 15 residues processed: 139 average time/residue: 0.0761 time to fit residues: 16.3872 Evaluate side-chains 135 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 757 TYR Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 101 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.1980 chunk 105 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN ** B 674 GLN ** 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 = 0.4965 r_free = 0.4965 target = 0.260176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.228854 restraints weight = 14325.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.228696 restraints weight = 11793.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.230746 restraints weight = 10756.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.231242 restraints weight = 7149.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.232677 restraints weight = 6773.632| |-----------------------------------------------------------------------------| r_work (final): 0.4718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10695 Z= 0.131 Angle : 0.641 13.991 14538 Z= 0.320 Chirality : 0.042 0.163 1612 Planarity : 0.005 0.059 1781 Dihedral : 4.491 28.733 1396 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.08 % Allowed : 23.06 % Favored : 74.86 % 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: -1.33 (0.24), residues: 1245 helix: 0.46 (0.19), residues: 737 sheet: -3.18 (1.96), residues: 10 loop : -3.01 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 478 TYR 0.015 0.001 TYR B 305 PHE 0.053 0.002 PHE B 852 TRP 0.018 0.001 TRP B 333 HIS 0.013 0.001 HIS B 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (10689) covalent geometry : angle 0.64101 / 0.32 (14526) SS BOND : bond 0.00134 / 0.08 ( 6) SS BOND : angle 0.66497 / 0.38 ( 12) hydrogen bonds : bond 0.03967 / 2.60 ( 550) hydrogen bonds : angle 4.95882 / 3.45 ( 1632) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.406 Fit side-chains REVERT: A 373 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7714 (mt) REVERT: A 393 PHE cc_start: 0.4027 (OUTLIER) cc_final: 0.3236 (p90) REVERT: A 506 GLN cc_start: 0.6250 (OUTLIER) cc_final: 0.4471 (pm20) REVERT: A 678 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8476 (p) REVERT: B 678 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8441 (p) REVERT: B 748 SER cc_start: 0.8392 (p) cc_final: 0.7960 (t) outliers start: 23 outliers final: 17 residues processed: 139 average time/residue: 0.0758 time to fit residues: 16.4658 Evaluate side-chains 142 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 757 TYR Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 10 optimal weight: 0.1980 chunk 23 optimal weight: 3.9990 chunk 115 optimal weight: 0.0040 chunk 14 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN ** B 674 GLN ** 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 = 0.4972 r_free = 0.4972 target = 0.260732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.229670 restraints weight = 14304.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.228783 restraints weight = 11842.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.230795 restraints weight = 11333.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.231504 restraints weight = 7662.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.232055 restraints weight = 7051.398| |-----------------------------------------------------------------------------| r_work (final): 0.4757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10695 Z= 0.128 Angle : 0.650 14.083 14538 Z= 0.321 Chirality : 0.042 0.162 1612 Planarity : 0.005 0.059 1781 Dihedral : 4.446 27.950 1396 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.17 % Allowed : 22.88 % Favored : 74.95 % 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: -1.28 (0.24), residues: 1245 helix: 0.50 (0.19), residues: 741 sheet: -3.19 (1.96), residues: 10 loop : -3.02 (0.24), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 478 TYR 0.045 0.001 TYR B 847 PHE 0.053 0.001 PHE B 852 TRP 0.018 0.001 TRP B 333 HIS 0.013 0.001 HIS B 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (10689) covalent geometry : angle 0.64957 / 0.32 (14526) SS BOND : bond 0.00126 / 0.08 ( 6) SS BOND : angle 0.60667 / 0.36 ( 12) hydrogen bonds : bond 0.03897 / 2.57 ( 550) hydrogen bonds : angle 4.92055 / 3.42 ( 1632) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1600.67 seconds wall clock time: 28 minutes 30.30 seconds (1710.30 seconds total)