Starting phenix.real_space_refine on Wed Mar 12 09:02:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yah_33712/03_2025/7yah_33712.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yah_33712/03_2025/7yah_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_33712/03_2025/7yah_33712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yah_33712/03_2025/7yah_33712.map" model { file = "/net/cci-nas-00/data/ceres_data/7yah_33712/03_2025/7yah_33712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yah_33712/03_2025/7yah_33712.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.66, per 1000 atoms: 0.61 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: 2.12 Conformation dependent library (CDL) restraints added in 953.3 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: 1.09 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: 3.24 Time building geometry restraints manager: 2.49 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: 4451 26.38 - 52.75: 251 52.75 - 79.13: 26 79.13 - 105.51: 4 105.51 - 131.88: 1 Dihedral angle restraints: 4733 sinusoidal: 1867 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 4730 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: 0.010 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.400 Find NCS groups from input model: 0.090 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 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 7793 Z= 0.392 Angle : 0.841 14.791 10555 Z= 0.504 Chirality : 0.053 0.326 1248 Planarity : 0.005 0.051 1328 Dihedral : 15.971 131.883 2884 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.021 0.001 TRP A 460 HIS 0.002 0.001 HIS C 86 PHE 0.023 0.002 PHE A 57 TYR 0.023 0.002 TYR C 112 ARG 0.013 0.001 ARG A 403 *********************** 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 : 1.003 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: 0.1874 time to fit residues: 24.9331 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 : 0.766 ------------------------------------------------------------------------------- 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 83 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 89 optimal weight: 20.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 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 = 0.4469 r_free = 0.4469 target = 0.222497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.184841 restraints weight = 7150.906| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 1.99 r_work: 0.3671 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7793 Z= 0.199 Angle : 0.525 7.034 10555 Z= 0.281 Chirality : 0.041 0.138 1248 Planarity : 0.004 0.054 1328 Dihedral : 8.145 121.134 1094 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.07 % Allowed : 17.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 989 helix: 1.37 (0.22), residues: 503 sheet: 0.12 (0.46), residues: 117 loop : -0.09 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 66 HIS 0.001 0.000 HIS A 140 PHE 0.014 0.001 PHE A 861 TYR 0.015 0.001 TYR C 112 ARG 0.004 0.000 ARG A 403 *********************** 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 119 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.742 Fit side-chains REVERT: A 100 PHE cc_start: 0.6190 (OUTLIER) cc_final: 0.5372 (t80) outliers start: 26 outliers final: 13 residues processed: 110 average time/residue: 0.1734 time to fit residues: 27.1776 Evaluate side-chains 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 219 MET 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 1 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 32 optimal weight: 0.0980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4443 r_free = 0.4443 target = 0.219291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.189643 restraints weight = 7285.809| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 1.53 r_work: 0.3770 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7793 Z= 0.297 Angle : 0.573 7.082 10555 Z= 0.303 Chirality : 0.042 0.137 1248 Planarity : 0.005 0.063 1328 Dihedral : 8.125 125.787 1094 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.37 % Allowed : 17.85 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 989 helix: 1.35 (0.23), residues: 501 sheet: -0.01 (0.45), residues: 117 loop : -0.11 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 460 HIS 0.002 0.001 HIS A 98 PHE 0.015 0.002 PHE A 812 TYR 0.012 0.001 TYR A 696 ARG 0.005 0.000 ARG A 403 *********************** 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 125 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 0.804 Fit side-chains REVERT: A 85 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6883 (mtt) REVERT: A 100 PHE cc_start: 0.6394 (OUTLIER) cc_final: 0.5662 (t80) REVERT: A 477 CYS cc_start: 0.5143 (OUTLIER) cc_final: 0.4829 (p) outliers start: 37 outliers final: 20 residues processed: 112 average time/residue: 0.1723 time to fit residues: 27.6563 Evaluate side-chains 108 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 343 CYS Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 502 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 19 optimal weight: 0.7980 chunk 94 optimal weight: 50.0000 chunk 86 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 88 optimal weight: 50.0000 chunk 7 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4464 r_free = 0.4464 target = 0.221901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.184007 restraints weight = 7219.507| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.00 r_work: 0.3660 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7793 Z= 0.190 Angle : 0.511 7.083 10555 Z= 0.272 Chirality : 0.040 0.137 1248 Planarity : 0.004 0.062 1328 Dihedral : 7.896 118.108 1094 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.43 % Allowed : 19.03 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.27), residues: 989 helix: 1.72 (0.23), residues: 503 sheet: 0.15 (0.42), residues: 135 loop : -0.04 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 66 HIS 0.001 0.000 HIS A 372 PHE 0.023 0.001 PHE A 812 TYR 0.010 0.001 TYR C 112 ARG 0.005 0.000 ARG A 403 *********************** 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 122 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8036 (mt) cc_final: 0.7584 (tp) REVERT: A 85 MET cc_start: 0.7236 (mtm) cc_final: 0.6985 (mtt) REVERT: A 100 PHE cc_start: 0.6243 (OUTLIER) cc_final: 0.5703 (t80) REVERT: A 159 ASP cc_start: 0.6364 (OUTLIER) cc_final: 0.5434 (t0) outliers start: 29 outliers final: 20 residues processed: 111 average time/residue: 0.1614 time to fit residues: 26.0176 Evaluate side-chains 106 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 134 LEU 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 219 MET 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 393 VAL 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 544 ILE Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 871 GLU 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 60 optimal weight: 0.0570 chunk 17 optimal weight: 0.8980 chunk 87 optimal weight: 30.0000 chunk 35 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4478 r_free = 0.4478 target = 0.223673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.186023 restraints weight = 7203.744| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 1.97 r_work: 0.3690 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7793 Z= 0.159 Angle : 0.506 9.331 10555 Z= 0.264 Chirality : 0.039 0.136 1248 Planarity : 0.004 0.060 1328 Dihedral : 7.776 116.424 1094 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.78 % Allowed : 20.09 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.27), residues: 989 helix: 1.95 (0.23), residues: 503 sheet: 0.76 (0.43), residues: 134 loop : -0.08 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 66 HIS 0.001 0.000 HIS A 372 PHE 0.019 0.001 PHE A 812 TYR 0.009 0.001 TYR A 696 ARG 0.002 0.000 ARG A 403 *********************** 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 : 0.767 Fit side-chains REVERT: A 29 LEU cc_start: 0.8070 (mt) cc_final: 0.7691 (tp) REVERT: A 85 MET cc_start: 0.7271 (OUTLIER) cc_final: 0.7056 (mtt) REVERT: A 100 PHE cc_start: 0.6257 (OUTLIER) cc_final: 0.5751 (t80) outliers start: 32 outliers final: 22 residues processed: 111 average time/residue: 0.1626 time to fit residues: 26.3804 Evaluate side-chains 108 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 181 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 255 LYS 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 393 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 420 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 17 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 92 optimal weight: 20.0000 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4446 r_free = 0.4446 target = 0.219881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.187915 restraints weight = 7256.426| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 1.61 r_work: 0.3759 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7793 Z= 0.267 Angle : 0.577 13.174 10555 Z= 0.298 Chirality : 0.042 0.137 1248 Planarity : 0.005 0.063 1328 Dihedral : 7.900 120.504 1092 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.73 % Allowed : 19.50 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.27), residues: 989 helix: 1.64 (0.23), residues: 502 sheet: 0.60 (0.43), residues: 140 loop : -0.09 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 460 HIS 0.002 0.001 HIS A 98 PHE 0.023 0.002 PHE A 812 TYR 0.011 0.001 TYR A 696 ARG 0.004 0.000 ARG A 523 *********************** 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 128 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 88 time to evaluate : 0.791 Fit side-chains REVERT: A 29 LEU cc_start: 0.7834 (mt) cc_final: 0.7606 (tp) REVERT: A 85 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.6796 (mtt) REVERT: A 100 PHE cc_start: 0.6211 (OUTLIER) cc_final: 0.5574 (t80) REVERT: A 159 ASP cc_start: 0.6408 (OUTLIER) cc_final: 0.5412 (t0) REVERT: A 810 MET cc_start: 0.7818 (mmm) cc_final: 0.7606 (mmm) outliers start: 40 outliers final: 27 residues processed: 120 average time/residue: 0.1553 time to fit residues: 27.5733 Evaluate side-chains 115 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 160 THR 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 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 682 PHE Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 769 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 12 optimal weight: 0.0040 chunk 28 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 0.0770 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 98 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 overall best weight: 0.4950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4472 r_free = 0.4472 target = 0.223163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.183763 restraints weight = 7215.969| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 2.03 r_work: 0.3675 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7793 Z= 0.160 Angle : 0.532 14.983 10555 Z= 0.273 Chirality : 0.041 0.343 1248 Planarity : 0.004 0.058 1328 Dihedral : 7.711 115.393 1092 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.78 % Allowed : 20.09 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.27), residues: 989 helix: 1.86 (0.23), residues: 503 sheet: 0.68 (0.43), residues: 140 loop : -0.06 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 460 HIS 0.005 0.001 HIS A 149 PHE 0.018 0.001 PHE A 812 TYR 0.009 0.001 TYR A 696 ARG 0.005 0.000 ARG A 403 *********************** 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: 32 poor density : 86 time to evaluate : 0.836 Fit side-chains REVERT: A 29 LEU cc_start: 0.7763 (mt) cc_final: 0.7453 (tp) REVERT: A 85 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.7025 (mtt) REVERT: A 100 PHE cc_start: 0.6171 (OUTLIER) cc_final: 0.5611 (t80) REVERT: A 159 ASP cc_start: 0.6297 (OUTLIER) cc_final: 0.5296 (t0) REVERT: A 541 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8146 (mp) REVERT: C 67 MET cc_start: 0.8891 (ptp) cc_final: 0.8337 (pmm) outliers start: 32 outliers final: 26 residues processed: 107 average time/residue: 0.1639 time to fit residues: 25.5273 Evaluate side-chains 114 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 181 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 255 LYS 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 420 THR 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 704 ARG 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 1 optimal weight: 0.0170 chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 34 optimal weight: 0.0020 overall best weight: 0.6228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4474 r_free = 0.4474 target = 0.223483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.184073 restraints weight = 7278.870| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.10 r_work: 0.3644 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7793 Z= 0.166 Angle : 0.533 16.123 10555 Z= 0.272 Chirality : 0.041 0.323 1248 Planarity : 0.004 0.058 1328 Dihedral : 7.693 115.561 1092 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.02 % Allowed : 19.86 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.27), residues: 989 helix: 1.93 (0.23), residues: 502 sheet: 0.73 (0.43), residues: 140 loop : -0.08 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 460 HIS 0.003 0.001 HIS A 149 PHE 0.017 0.001 PHE A 812 TYR 0.009 0.001 TYR A 696 ARG 0.006 0.000 ARG A 403 *********************** 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 119 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 0.804 Fit side-chains REVERT: A 85 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.7132 (mtt) REVERT: A 100 PHE cc_start: 0.6213 (OUTLIER) cc_final: 0.5646 (t80) REVERT: A 159 ASP cc_start: 0.6407 (OUTLIER) cc_final: 0.5422 (t0) REVERT: C 67 MET cc_start: 0.8919 (ptp) cc_final: 0.8388 (pmm) outliers start: 34 outliers final: 28 residues processed: 106 average time/residue: 0.1684 time to fit residues: 25.6675 Evaluate side-chains 113 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 181 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 255 LYS 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 420 THR 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 704 ARG Chi-restraints excluded: chain A residue 769 SER 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 23 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4465 r_free = 0.4465 target = 0.222329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.177759 restraints weight = 7335.659| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.94 r_work: 0.3664 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7793 Z= 0.208 Angle : 0.550 15.754 10555 Z= 0.281 Chirality : 0.041 0.309 1248 Planarity : 0.004 0.058 1328 Dihedral : 7.750 117.290 1092 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.02 % Allowed : 19.98 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.27), residues: 989 helix: 1.87 (0.23), residues: 502 sheet: 0.71 (0.43), residues: 140 loop : -0.12 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 460 HIS 0.004 0.001 HIS A 149 PHE 0.019 0.001 PHE A 812 TYR 0.009 0.001 TYR A 696 ARG 0.009 0.000 ARG A 174 *********************** 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 117 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 0.774 Fit side-chains REVERT: A 85 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.7017 (mtt) REVERT: A 100 PHE cc_start: 0.6090 (OUTLIER) cc_final: 0.5524 (t80) REVERT: A 159 ASP cc_start: 0.6361 (OUTLIER) cc_final: 0.5311 (t0) REVERT: C 67 MET cc_start: 0.8924 (ptp) cc_final: 0.8384 (pmm) outliers start: 34 outliers final: 26 residues processed: 106 average time/residue: 0.1561 time to fit residues: 24.1249 Evaluate side-chains 111 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 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 704 ARG Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 769 SER 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 13 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 38 optimal weight: 0.2980 chunk 97 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4472 r_free = 0.4472 target = 0.223254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.184576 restraints weight = 7273.036| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 1.96 r_work: 0.3691 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7793 Z= 0.179 Angle : 0.539 14.904 10555 Z= 0.276 Chirality : 0.041 0.301 1248 Planarity : 0.004 0.057 1328 Dihedral : 7.713 116.326 1092 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.78 % Allowed : 20.33 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.27), residues: 989 helix: 1.91 (0.23), residues: 502 sheet: 0.71 (0.43), residues: 140 loop : -0.13 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 460 HIS 0.002 0.000 HIS A 149 PHE 0.018 0.001 PHE A 812 TYR 0.009 0.001 TYR A 696 ARG 0.007 0.000 ARG A 174 ********************** 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 116 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.829 Fit side-chains REVERT: A 85 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6993 (mtt) REVERT: A 100 PHE cc_start: 0.6120 (OUTLIER) cc_final: 0.5533 (t80) REVERT: A 159 ASP cc_start: 0.6369 (OUTLIER) cc_final: 0.5337 (t0) REVERT: A 686 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.6378 (tpp) REVERT: C 67 MET cc_start: 0.8929 (ptp) cc_final: 0.8428 (pmm) outliers start: 32 outliers final: 26 residues processed: 106 average time/residue: 0.1585 time to fit residues: 24.8557 Evaluate side-chains 113 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 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 686 MET Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 769 SER 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 26 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 55 optimal weight: 0.3980 chunk 71 optimal weight: 0.6980 chunk 94 optimal weight: 30.0000 chunk 33 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4470 r_free = 0.4470 target = 0.223024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.187055 restraints weight = 7222.573| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 1.82 r_work: 0.3694 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7793 Z= 0.186 Angle : 0.543 15.239 10555 Z= 0.278 Chirality : 0.041 0.295 1248 Planarity : 0.004 0.056 1328 Dihedral : 7.722 116.444 1092 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.90 % Allowed : 20.45 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.27), residues: 989 helix: 1.88 (0.23), residues: 502 sheet: 0.91 (0.44), residues: 134 loop : -0.21 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 460 HIS 0.001 0.000 HIS A 98 PHE 0.018 0.001 PHE A 812 TYR 0.009 0.001 TYR A 696 ARG 0.008 0.000 ARG A 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3718.33 seconds wall clock time: 65 minutes 31.14 seconds (3931.14 seconds total)