Starting phenix.real_space_refine on Thu Jul 2 07:42:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yah_33712/07_2026/7yah_33712.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yah_33712/07_2026/7yah_33712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yah_33712/07_2026/7yah_33712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yah_33712/07_2026/7yah_33712.map" model { file = "/net/cci-nas-00/data/ceres_data/7yah_33712/07_2026/7yah_33712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yah_33712/07_2026/7yah_33712.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yah_33712/07_2026/7yah_33712.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yah_33712/07_2026/7yah_33712.cif" } resolution = 3.12 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= 0.005 sd= 0.060 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 3 5.49 5 S 55 5.16 5 C 4872 2.51 5 N 1285 2.21 5 O 1450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 7666 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 876, 6692 Classifications: {'peptide': 876} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 34, 'TRANS': 841} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.46, per 1000 atoms: 0.19 Number of scatterers: 7666 At special positions: 0 Unit cell: (84.71, 80.77, 134.945, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 55 16.00 P 3 15.00 O 1450 8.00 N 1285 7.00 C 4872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 128 " 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: 0.47 Conformation dependent library (CDL) restraints added in 409.0 milliseconds 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1846 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 9 sheets defined 51.1% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 30 through 38 Processing helix chain 'A' and resid 47 through 58 Processing helix chain 'A' and resid 71 through 78 Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 99 through 135 Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.830A pdb=" N ASN A 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER A 239 " --> pdb=" O GLY A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 235 through 239' Processing helix chain 'A' and resid 241 through 250 removed outlier: 4.033A pdb=" N PHE A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 288 removed outlier: 3.500A pdb=" N ASP A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 308 through 328 removed outlier: 4.296A pdb=" N ILE A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 removed outlier: 4.292A pdb=" N GLU A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 398 through 412 removed outlier: 3.962A pdb=" N ASN A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 438 removed outlier: 3.631A pdb=" N LEU A 430 " --> pdb=" O THR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.645A pdb=" N LEU A 442 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 Processing helix chain 'A' and resid 503 through 520 Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 573 through 585 Processing helix chain 'A' and resid 596 through 602 Processing helix chain 'A' and resid 603 through 611 Processing helix chain 'A' and resid 621 through 635 Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 666 through 673 Processing helix chain 'A' and resid 682 through 723 removed outlier: 3.822A pdb=" N MET A 686 " --> pdb=" O PHE A 682 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR A 696 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 743 Processing helix chain 'A' and resid 743 through 751 removed outlier: 3.850A pdb=" N LEU A 749 " --> pdb=" O PRO A 745 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 799 Processing helix chain 'A' and resid 804 through 825 removed outlier: 3.754A pdb=" N THR A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 837 Processing helix chain 'A' and resid 841 through 861 Processing helix chain 'A' and resid 861 through 869 Processing helix chain 'A' and resid 874 through 886 Processing helix chain 'A' and resid 886 through 904 Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 151 removed outlier: 4.194A pdb=" N HIS A 140 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL A 223 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER A 182 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N CYS A 225 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASP A 180 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LYS A 227 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ALA A 178 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS A 229 " --> pdb=" O PHE A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 151 removed outlier: 4.194A pdb=" N HIS A 140 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL A 223 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER A 182 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N CYS A 225 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASP A 180 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LYS A 227 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ALA A 178 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS A 229 " --> pdb=" O PHE A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 330 through 332 removed outlier: 6.847A pdb=" N VAL A 639 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL A 659 " --> pdb=" O VAL A 639 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N MET A 641 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N MET A 661 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL A 346 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N THR A 642 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N CYS A 348 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE A 566 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N PHE A 617 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N MET A 568 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLN A 592 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE A 617 " --> pdb=" O GLN A 592 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 594 " --> pdb=" O PHE A 617 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 393 removed outlier: 4.738A pdb=" N VAL A 386 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS A 364 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU A 536 " --> pdb=" O PRO A 531 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N PHE A 538 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER A 529 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A 540 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 450 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL A 466 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ARG A 448 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 393 removed outlier: 4.738A pdb=" N VAL A 386 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS A 364 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU A 536 " --> pdb=" O CYS A 490 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN A 494 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N GLY A 540 " --> pdb=" O GLN A 494 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 416 through 417 Processing sheet with id=AA7, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.707A pdb=" N ASP C 105 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.617A pdb=" N TRP C 69 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLY C 83 " --> pdb=" O MET C 67 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET C 67 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TRP C 66 " --> pdb=" O GLN C 131 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU C 146 " --> pdb=" O TYR C 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.617A pdb=" N TRP C 69 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLY C 83 " --> pdb=" O MET C 67 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET C 67 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TRP C 66 " --> pdb=" O GLN C 131 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1404 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: 1.16 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1444 1.33 - 1.45: 1777 1.45 - 1.57: 4480 1.57 - 1.69: 2 1.69 - 1.81: 90 Bond restraints: 7793 Sorted by residual: bond pdb=" O3A ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sigma weight residual 1.698 1.599 0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C3B ACP A1001 " pdb=" PG ACP A1001 " ideal model delta sigma weight residual 1.875 1.793 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" O5' ACP A1001 " pdb=" PA ACP A1001 " ideal model delta sigma weight residual 1.659 1.579 0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C LEU A 335 " pdb=" N PRO A 336 " ideal model delta sigma weight residual 1.336 1.370 -0.034 1.08e-02 8.57e+03 1.00e+01 bond pdb=" CA SER A 687 " pdb=" CB SER A 687 " ideal model delta sigma weight residual 1.528 1.481 0.048 1.56e-02 4.11e+03 9.28e+00 ... (remaining 7788 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 10411 2.96 - 5.92: 126 5.92 - 8.87: 15 8.87 - 11.83: 2 11.83 - 14.79: 1 Bond angle restraints: 10555 Sorted by residual: angle pdb=" PA ACP A1001 " pdb=" O3A ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sigma weight residual 125.06 110.27 14.79 3.00e+00 1.11e-01 2.43e+01 angle pdb=" N MET A 97 " pdb=" CA MET A 97 " pdb=" C MET A 97 " ideal model delta sigma weight residual 108.17 100.87 7.30 1.85e+00 2.92e-01 1.56e+01 angle pdb=" N MET A 262 " pdb=" CA MET A 262 " pdb=" C MET A 262 " ideal model delta sigma weight residual 112.89 108.09 4.80 1.24e+00 6.50e-01 1.50e+01 angle pdb=" CA MET A 97 " pdb=" C MET A 97 " pdb=" O MET A 97 " ideal model delta sigma weight residual 121.66 117.21 4.45 1.17e+00 7.31e-01 1.45e+01 angle pdb=" C SER A 825 " pdb=" N SER A 826 " pdb=" CA SER A 826 " ideal model delta sigma weight residual 122.54 116.30 6.24 1.65e+00 3.67e-01 1.43e+01 ... (remaining 10550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.38: 4444 26.38 - 52.75: 241 52.75 - 79.13: 15 79.13 - 105.51: 4 105.51 - 131.88: 1 Dihedral angle restraints: 4705 sinusoidal: 1839 harmonic: 2866 Sorted by residual: dihedral pdb=" O1A ACP A1001 " pdb=" O3A ACP A1001 " pdb=" PA ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sinusoidal sigma weight residual -48.75 83.13 -131.88 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" CA PHE A 861 " pdb=" C PHE A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta harmonic sigma weight residual 180.00 -161.62 -18.38 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" O1B ACP A1001 " pdb=" C3B ACP A1001 " pdb=" PB ACP A1001 " pdb=" PG ACP A1001 " ideal model delta sinusoidal sigma weight residual -52.82 50.74 -103.56 1 3.00e+01 1.11e-03 1.32e+01 ... (remaining 4702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1035 0.065 - 0.130: 180 0.130 - 0.196: 26 0.196 - 0.261: 6 0.261 - 0.326: 1 Chirality restraints: 1248 Sorted by residual: chirality pdb=" CA MET A 97 " pdb=" N MET A 97 " pdb=" C MET A 97 " pdb=" CB MET A 97 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA MET A 686 " pdb=" N MET A 686 " pdb=" C MET A 686 " pdb=" CB MET A 686 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA GLN A 99 " pdb=" N GLN A 99 " pdb=" C GLN A 99 " pdb=" CB GLN A 99 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1245 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 822 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.42e+00 pdb=" C ASN A 822 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN A 822 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA A 823 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 97 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.67e+00 pdb=" C MET A 97 " -0.045 2.00e-02 2.50e+03 pdb=" O MET A 97 " 0.017 2.00e-02 2.50e+03 pdb=" N HIS A 98 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 260 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C LYS A 260 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS A 260 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 261 " 0.013 2.00e-02 2.50e+03 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1285 2.76 - 3.30: 7515 3.30 - 3.83: 13097 3.83 - 4.37: 15657 4.37 - 4.90: 26775 Nonbonded interactions: 64329 Sorted by model distance: nonbonded pdb=" OG1 THR A 570 " pdb=" O PHE A 617 " model vdw 2.229 3.040 nonbonded pdb=" O LEU A 884 " pdb=" OG SER A 887 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR A 352 " pdb=" O3G ACP A1001 " model vdw 2.258 3.040 nonbonded pdb=" O GLY A 395 " pdb=" OG SER A 402 " model vdw 2.260 3.040 nonbonded pdb=" OG SER C 142 " pdb=" OD1 ASP C 144 " model vdw 2.279 3.040 ... (remaining 64324 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.160 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 7794 Z= 0.334 Angle : 0.840 14.791 10557 Z= 0.504 Chirality : 0.053 0.326 1248 Planarity : 0.005 0.051 1328 Dihedral : 15.382 131.883 2856 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.35 % Allowed : 19.27 % Favored : 80.38 % 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: 0.05 (0.25), residues: 989 helix: 0.33 (0.22), residues: 498 sheet: 0.29 (0.45), residues: 122 loop : -0.27 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 403 TYR 0.023 0.002 TYR C 112 PHE 0.023 0.002 PHE A 57 TRP 0.021 0.001 TRP A 460 HIS 0.002 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.33 ( 7793) covalent geometry : angle 0.84055 / 0.50 (10555) SS BOND : bond 0.00111 / 0.06 ( 1) SS BOND : angle 0.11014 / 0.06 ( 2) hydrogen bonds : bond 0.12750 / 8.28 ( 447) hydrogen bonds : angle 6.24060 / 4.39 ( 1404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.198 Fit side-chains REVERT: A 100 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.6195 (t80) outliers start: 3 outliers final: 1 residues processed: 95 average time/residue: 0.0708 time to fit residues: 9.5704 Evaluate side-chains 89 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 149 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.222801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.192701 restraints weight = 7229.011| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 1.58 r_work: 0.3816 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7794 Z= 0.134 Angle : 0.525 6.922 10557 Z= 0.281 Chirality : 0.040 0.141 1248 Planarity : 0.004 0.051 1328 Dihedral : 6.655 117.532 1066 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.31 % Allowed : 17.49 % Favored : 79.20 % 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: 0.95 (0.26), residues: 989 helix: 1.36 (0.22), residues: 503 sheet: 0.11 (0.46), residues: 117 loop : -0.09 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.014 0.001 TYR C 112 PHE 0.013 0.001 PHE A 861 TRP 0.008 0.001 TRP C 66 HIS 0.001 0.000 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 7793) covalent geometry : angle 0.52510 / 0.28 (10555) SS BOND : bond 0.00070 / 0.04 ( 1) SS BOND : angle 0.15606 / 0.09 ( 2) hydrogen bonds : bond 0.04096 / 2.71 ( 447) hydrogen bonds : angle 4.62773 / 3.19 ( 1404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.259 Fit side-chains REVERT: A 100 PHE cc_start: 0.6252 (OUTLIER) cc_final: 0.5465 (t80) outliers start: 28 outliers final: 12 residues processed: 112 average time/residue: 0.0625 time to fit residues: 9.9003 Evaluate side-chains 97 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain C residue 115 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.0770 chunk 94 optimal weight: 50.0000 chunk 73 optimal weight: 0.0050 chunk 40 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.4352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.225446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.186746 restraints weight = 7173.022| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 1.96 r_work: 0.3705 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7794 Z= 0.108 Angle : 0.491 7.135 10557 Z= 0.262 Chirality : 0.039 0.140 1248 Planarity : 0.004 0.058 1328 Dihedral : 6.387 111.758 1066 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.96 % Allowed : 17.73 % Favored : 79.31 % 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: 1.44 (0.27), residues: 989 helix: 1.89 (0.23), residues: 503 sheet: 0.09 (0.45), residues: 123 loop : 0.03 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.011 0.001 TYR C 112 PHE 0.013 0.001 PHE A 861 TRP 0.006 0.001 TRP C 66 HIS 0.001 0.000 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 7793) covalent geometry : angle 0.49142 / 0.26 (10555) SS BOND : bond 0.00093 / 0.05 ( 1) SS BOND : angle 0.16125 / 0.08 ( 2) hydrogen bonds : bond 0.03567 / 2.37 ( 447) hydrogen bonds : angle 4.20920 / 2.89 ( 1404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.261 Fit side-chains REVERT: A 29 LEU cc_start: 0.8180 (mt) cc_final: 0.7743 (tp) REVERT: A 100 PHE cc_start: 0.6221 (OUTLIER) cc_final: 0.5595 (t80) outliers start: 25 outliers final: 12 residues processed: 107 average time/residue: 0.0608 time to fit residues: 9.6427 Evaluate side-chains 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain C residue 115 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 91 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.219664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.187956 restraints weight = 7278.715| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 1.62 r_work: 0.3750 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7794 Z= 0.194 Angle : 0.565 7.017 10557 Z= 0.296 Chirality : 0.042 0.140 1248 Planarity : 0.005 0.063 1328 Dihedral : 6.666 119.869 1066 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.37 % Allowed : 17.02 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.27), residues: 989 helix: 1.62 (0.23), residues: 502 sheet: 0.35 (0.41), residues: 141 loop : -0.04 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 523 TYR 0.010 0.001 TYR A 696 PHE 0.015 0.002 PHE A 812 TRP 0.012 0.001 TRP A 460 HIS 0.002 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 ( 7793) covalent geometry : angle 0.56533 / 0.30 (10555) SS BOND : bond 0.00049 / 0.03 ( 1) SS BOND : angle 0.01247 / 0.01 ( 2) hydrogen bonds : bond 0.04197 / 2.76 ( 447) hydrogen bonds : angle 4.48366 / 3.09 ( 1404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.166 Fit side-chains REVERT: A 29 LEU cc_start: 0.8304 (mt) cc_final: 0.7948 (tp) REVERT: A 85 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6890 (mtt) REVERT: A 100 PHE cc_start: 0.6312 (OUTLIER) cc_final: 0.5660 (t80) outliers start: 37 outliers final: 23 residues processed: 115 average time/residue: 0.0577 time to fit residues: 9.7459 Evaluate side-chains 112 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain C residue 115 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 4 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.0970 chunk 96 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 94 optimal weight: 30.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 238 ASN ** A 412 ASN ** 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 = 0.4475 r_free = 0.4475 target = 0.223190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.183601 restraints weight = 7262.877| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 2.18 r_work: 0.3678 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7794 Z= 0.118 Angle : 0.506 7.203 10557 Z= 0.268 Chirality : 0.040 0.142 1248 Planarity : 0.004 0.059 1328 Dihedral : 6.473 115.273 1066 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.78 % Allowed : 19.15 % Favored : 77.07 % 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 (0.27), residues: 989 helix: 1.86 (0.23), residues: 503 sheet: 0.50 (0.42), residues: 140 loop : -0.02 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 403 TYR 0.009 0.001 TYR C 112 PHE 0.021 0.001 PHE A 812 TRP 0.010 0.001 TRP A 460 HIS 0.001 0.000 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 7793) covalent geometry : angle 0.50630 / 0.27 (10555) SS BOND : bond 0.00103 / 0.05 ( 1) SS BOND : angle 0.17202 / 0.09 ( 2) hydrogen bonds : bond 0.03667 / 2.44 ( 447) hydrogen bonds : angle 4.19731 / 2.89 ( 1404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.193 Fit side-chains REVERT: A 29 LEU cc_start: 0.7736 (mt) cc_final: 0.7476 (tp) REVERT: A 85 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6987 (mtt) REVERT: A 100 PHE cc_start: 0.6199 (OUTLIER) cc_final: 0.5700 (t80) REVERT: A 159 ASP cc_start: 0.6341 (OUTLIER) cc_final: 0.5325 (t0) REVERT: A 271 PHE cc_start: 0.6251 (m-10) cc_final: 0.6051 (m-10) outliers start: 32 outliers final: 22 residues processed: 111 average time/residue: 0.0547 time to fit residues: 8.8799 Evaluate side-chains 109 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 82 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 chunk 95 optimal weight: 40.0000 chunk 31 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 57 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.223823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.187183 restraints weight = 7267.018| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 1.68 r_work: 0.3725 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7794 Z= 0.114 Angle : 0.492 7.115 10557 Z= 0.259 Chirality : 0.039 0.137 1248 Planarity : 0.004 0.053 1328 Dihedral : 6.374 114.486 1066 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.02 % Allowed : 18.91 % Favored : 77.07 % 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: 1.58 (0.27), residues: 989 helix: 1.99 (0.23), residues: 503 sheet: 0.40 (0.42), residues: 134 loop : -0.00 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.009 0.001 TYR C 127 PHE 0.020 0.001 PHE A 812 TRP 0.011 0.001 TRP A 460 HIS 0.001 0.000 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 7793) covalent geometry : angle 0.49167 / 0.26 (10555) SS BOND : bond 0.00087 / 0.05 ( 1) SS BOND : angle 0.16032 / 0.09 ( 2) hydrogen bonds : bond 0.03534 / 2.34 ( 447) hydrogen bonds : angle 4.09578 / 2.82 ( 1404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 0.172 Fit side-chains REVERT: A 29 LEU cc_start: 0.7867 (mt) cc_final: 0.7628 (tp) REVERT: A 85 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6999 (mtt) REVERT: A 100 PHE cc_start: 0.6194 (OUTLIER) cc_final: 0.5673 (t80) REVERT: A 159 ASP cc_start: 0.6363 (OUTLIER) cc_final: 0.5355 (t0) REVERT: A 541 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8148 (mp) outliers start: 34 outliers final: 23 residues processed: 113 average time/residue: 0.0535 time to fit residues: 8.8806 Evaluate side-chains 111 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 0.0270 chunk 9 optimal weight: 0.8980 chunk 88 optimal weight: 50.0000 chunk 46 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 HIS ** A 412 ASN ** 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 = 0.4462 r_free = 0.4462 target = 0.221896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.192694 restraints weight = 7237.353| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 1.67 r_work: 0.3779 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7794 Z= 0.145 Angle : 0.526 7.920 10557 Z= 0.276 Chirality : 0.041 0.326 1248 Planarity : 0.004 0.054 1328 Dihedral : 6.353 117.178 1064 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.02 % Allowed : 19.27 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.27), residues: 989 helix: 1.90 (0.23), residues: 503 sheet: 0.60 (0.42), residues: 140 loop : -0.06 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 403 TYR 0.010 0.001 TYR C 127 PHE 0.022 0.001 PHE A 812 TRP 0.011 0.001 TRP A 460 HIS 0.001 0.001 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 7793) covalent geometry : angle 0.52615 / 0.28 (10555) SS BOND : bond 0.00129 / 0.07 ( 1) SS BOND : angle 0.20477 / 0.11 ( 2) hydrogen bonds : bond 0.03789 / 2.50 ( 447) hydrogen bonds : angle 4.18854 / 2.89 ( 1404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 84 time to evaluate : 0.168 Fit side-chains REVERT: A 85 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6915 (mtt) REVERT: A 100 PHE cc_start: 0.6215 (OUTLIER) cc_final: 0.5534 (t80) REVERT: A 159 ASP cc_start: 0.6405 (OUTLIER) cc_final: 0.5448 (t0) outliers start: 34 outliers final: 27 residues processed: 109 average time/residue: 0.0575 time to fit residues: 9.2747 Evaluate side-chains 112 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 82 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 16 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 0.0020 chunk 89 optimal weight: 50.0000 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 HIS ** A 412 ASN ** 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 = 0.4466 r_free = 0.4466 target = 0.222256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.192962 restraints weight = 7299.515| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 1.68 r_work: 0.3785 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7794 Z= 0.134 Angle : 0.519 8.152 10557 Z= 0.272 Chirality : 0.041 0.342 1248 Planarity : 0.004 0.054 1328 Dihedral : 6.327 116.450 1064 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.14 % Allowed : 19.15 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.27), residues: 989 helix: 1.90 (0.23), residues: 503 sheet: 0.64 (0.43), residues: 140 loop : -0.07 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 403 TYR 0.009 0.001 TYR A 696 PHE 0.027 0.001 PHE A 812 TRP 0.009 0.001 TRP A 460 HIS 0.005 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 7793) covalent geometry : angle 0.51923 / 0.27 (10555) SS BOND : bond 0.00126 / 0.07 ( 1) SS BOND : angle 0.21055 / 0.12 ( 2) hydrogen bonds : bond 0.03716 / 2.45 ( 447) hydrogen bonds : angle 4.17638 / 2.87 ( 1404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.225 Fit side-chains REVERT: A 85 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6920 (mtt) REVERT: A 100 PHE cc_start: 0.6212 (OUTLIER) cc_final: 0.5660 (t80) REVERT: A 159 ASP cc_start: 0.6364 (OUTLIER) cc_final: 0.5395 (t0) REVERT: A 541 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8162 (mp) outliers start: 35 outliers final: 27 residues processed: 107 average time/residue: 0.0591 time to fit residues: 9.3019 Evaluate side-chains 112 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 89 optimal weight: 50.0000 chunk 80 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 34 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 HIS ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.222530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.193240 restraints weight = 7224.968| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 1.65 r_work: 0.3800 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7794 Z= 0.134 Angle : 0.523 8.683 10557 Z= 0.273 Chirality : 0.041 0.328 1248 Planarity : 0.004 0.054 1328 Dihedral : 6.317 116.469 1064 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.26 % Allowed : 19.39 % Favored : 76.36 % 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 (0.27), residues: 989 helix: 1.91 (0.23), residues: 502 sheet: 0.67 (0.43), residues: 140 loop : -0.08 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 403 TYR 0.009 0.001 TYR A 696 PHE 0.025 0.001 PHE A 812 TRP 0.008 0.001 TRP A 460 HIS 0.004 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 7793) covalent geometry : angle 0.52255 / 0.27 (10555) SS BOND : bond 0.00137 / 0.07 ( 1) SS BOND : angle 0.26241 / 0.14 ( 2) hydrogen bonds : bond 0.03687 / 2.43 ( 447) hydrogen bonds : angle 4.17491 / 2.87 ( 1404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 0.274 Fit side-chains REVERT: A 85 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6892 (mtt) REVERT: A 100 PHE cc_start: 0.6193 (OUTLIER) cc_final: 0.5641 (t80) REVERT: A 159 ASP cc_start: 0.6374 (OUTLIER) cc_final: 0.5369 (t0) REVERT: A 541 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8152 (mp) outliers start: 36 outliers final: 29 residues processed: 111 average time/residue: 0.0588 time to fit residues: 9.6279 Evaluate side-chains 114 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 81 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.221878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.192273 restraints weight = 7259.185| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 1.66 r_work: 0.3781 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7794 Z= 0.140 Angle : 0.527 8.666 10557 Z= 0.276 Chirality : 0.041 0.322 1248 Planarity : 0.004 0.056 1328 Dihedral : 6.345 116.859 1064 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.78 % Allowed : 19.62 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.49 (0.27), residues: 989 helix: 1.87 (0.23), residues: 502 sheet: 0.66 (0.43), residues: 140 loop : -0.12 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 403 TYR 0.009 0.001 TYR A 696 PHE 0.035 0.002 PHE A 812 TRP 0.009 0.001 TRP A 460 HIS 0.001 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 7793) covalent geometry : angle 0.52744 / 0.28 (10555) SS BOND : bond 0.00142 / 0.07 ( 1) SS BOND : angle 0.30642 / 0.17 ( 2) hydrogen bonds : bond 0.03729 / 2.46 ( 447) hydrogen bonds : angle 4.17641 / 2.87 ( 1404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.223 Fit side-chains REVERT: A 85 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6932 (mtt) REVERT: A 100 PHE cc_start: 0.6203 (OUTLIER) cc_final: 0.5649 (t80) REVERT: A 159 ASP cc_start: 0.6387 (OUTLIER) cc_final: 0.5387 (t0) outliers start: 32 outliers final: 29 residues processed: 106 average time/residue: 0.0571 time to fit residues: 9.0529 Evaluate side-chains 115 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 39 optimal weight: 0.0970 chunk 44 optimal weight: 0.4980 chunk 97 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 0.0570 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.224603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.187684 restraints weight = 7238.531| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 1.96 r_work: 0.3692 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7794 Z= 0.110 Angle : 0.500 8.565 10557 Z= 0.262 Chirality : 0.040 0.307 1248 Planarity : 0.004 0.055 1328 Dihedral : 6.132 112.019 1064 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.66 % Allowed : 19.86 % Favored : 76.48 % 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: 1.66 (0.27), residues: 989 helix: 2.03 (0.23), residues: 502 sheet: 0.74 (0.43), residues: 140 loop : -0.06 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 403 TYR 0.008 0.001 TYR A 696 PHE 0.030 0.001 PHE A 812 TRP 0.007 0.001 TRP A 460 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 7793) covalent geometry : angle 0.50027 / 0.26 (10555) SS BOND : bond 0.00163 / 0.09 ( 1) SS BOND : angle 0.44635 / 0.24 ( 2) hydrogen bonds : bond 0.03405 / 2.25 ( 447) hydrogen bonds : angle 4.00451 / 2.76 ( 1404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1359.76 seconds wall clock time: 24 minutes 1.46 seconds (1441.46 seconds total)