Starting phenix.real_space_refine on Wed Sep 17 09:25:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yah_33712/09_2025/7yah_33712.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yah_33712/09_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_33712/09_2025/7yah_33712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yah_33712/09_2025/7yah_33712.map" model { file = "/net/cci-nas-00/data/ceres_data/7yah_33712/09_2025/7yah_33712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yah_33712/09_2025/7yah_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-2.0-5805/lib/python3.9/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: 1.62, per 1000 atoms: 0.21 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: 0.58 Conformation dependent library (CDL) restraints added in 347.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.35 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: 1.72 Time building geometry restraints manager: 0.75 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: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.460 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.250 ------------------------------------------------------------------------------- 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 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 : 15.971 131.883 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00626 ( 7793) covalent geometry : angle 0.84055 (10555) SS BOND : bond 0.00111 ( 1) SS BOND : angle 0.11014 ( 2) hydrogen bonds : bond 0.12750 ( 447) hydrogen bonds : angle 6.24060 ( 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 : 0.284 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: 0.0808 time to fit residues: 10.8553 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 : 0.281 ------------------------------------------------------------------------------- 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: 0.5980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** A 609 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.223267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.183500 restraints weight = 7222.615| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 2.26 r_work: 0.3633 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.0899 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= 0.131 Angle : 0.521 6.963 10557 Z= 0.279 Chirality : 0.040 0.142 1248 Planarity : 0.004 0.053 1328 Dihedral : 8.212 119.277 1094 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.31 % Allowed : 17.38 % 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 aren not related in a simple way. whole: 0.99 (0.26), residues: 989 helix: 1.40 (0.22), residues: 503 sheet: 0.13 (0.46), residues: 117 loop : -0.07 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.014 0.001 TYR C 112 PHE 0.014 0.001 PHE A 861 TRP 0.008 0.001 TRP C 66 HIS 0.002 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 7793) covalent geometry : angle 0.52151 (10555) SS BOND : bond 0.00055 ( 1) SS BOND : angle 0.15139 ( 2) hydrogen bonds : bond 0.03997 ( 447) hydrogen bonds : angle 4.59348 ( 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 : 0.306 Fit side-chains REVERT: A 100 PHE cc_start: 0.6216 (OUTLIER) cc_final: 0.5405 (t80) outliers start: 28 outliers final: 12 residues processed: 111 average time/residue: 0.0804 time to fit residues: 12.7659 Evaluate side-chains 96 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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: 0.9990 chunk 94 optimal weight: 40.0000 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 0.0670 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- 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 = 0.4478 r_free = 0.4478 target = 0.223829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.184757 restraints weight = 7178.435| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 2.14 r_work: 0.3633 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1176 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= 0.121 Angle : 0.501 7.080 10557 Z= 0.267 Chirality : 0.040 0.140 1248 Planarity : 0.004 0.060 1328 Dihedral : 7.892 119.649 1094 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.19 % Allowed : 17.97 % Favored : 78.84 % 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 aren not related in a simple way. whole: 1.35 (0.27), residues: 989 helix: 1.79 (0.23), residues: 503 sheet: 0.14 (0.45), residues: 117 loop : 0.01 (0.34), residues: 369 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 0.007 0.001 TRP A 460 HIS 0.001 0.000 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7793) covalent geometry : angle 0.50121 (10555) SS BOND : bond 0.00076 ( 1) SS BOND : angle 0.11939 ( 2) hydrogen bonds : bond 0.03739 ( 447) hydrogen bonds : angle 4.29615 ( 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 118 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.289 Fit side-chains REVERT: A 100 PHE cc_start: 0.6278 (OUTLIER) cc_final: 0.5700 (t80) outliers start: 27 outliers final: 12 residues processed: 106 average time/residue: 0.0788 time to fit residues: 12.1003 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 : 0.306 ------------------------------------------------------------------------------- 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: 0.9990 chunk 71 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 69 optimal weight: 0.0870 chunk 28 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4482 r_free = 0.4482 target = 0.224225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.184442 restraints weight = 7248.772| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 2.03 r_work: 0.3698 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1368 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 : 0.490 7.042 10557 Z= 0.260 Chirality : 0.040 0.136 1248 Planarity : 0.004 0.059 1328 Dihedral : 7.799 118.284 1094 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.78 % Allowed : 17.61 % 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 aren not related in a simple way. whole: 1.58 (0.27), residues: 989 helix: 1.97 (0.23), residues: 503 sheet: 0.47 (0.43), residues: 129 loop : 0.03 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.010 0.001 TYR C 112 PHE 0.012 0.001 PHE A 812 TRP 0.008 0.001 TRP A 460 HIS 0.001 0.000 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7793) covalent geometry : angle 0.49004 (10555) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.12196 ( 2) hydrogen bonds : bond 0.03554 ( 447) hydrogen bonds : angle 4.14999 ( 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 126 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.290 Fit side-chains REVERT: A 85 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6879 (mtt) REVERT: A 100 PHE cc_start: 0.6207 (OUTLIER) cc_final: 0.5586 (t80) REVERT: A 271 PHE cc_start: 0.6275 (m-10) cc_final: 0.6068 (m-10) outliers start: 32 outliers final: 20 residues processed: 113 average time/residue: 0.0765 time to fit residues: 12.5739 Evaluate side-chains 104 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 96 LEU 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 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 611 VAL 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: 2.9990 chunk 60 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.4451 r_free = 0.4451 target = 0.220462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.191103 restraints weight = 7230.680| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 1.58 r_work: 0.3772 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7794 Z= 0.174 Angle : 0.550 7.146 10557 Z= 0.287 Chirality : 0.041 0.137 1248 Planarity : 0.005 0.061 1328 Dihedral : 7.997 122.166 1094 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.26 % Allowed : 18.44 % Favored : 77.30 % 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 aren not related in a simple way. whole: 1.35 (0.27), residues: 989 helix: 1.71 (0.23), residues: 502 sheet: 0.48 (0.42), residues: 140 loop : -0.03 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 403 TYR 0.010 0.001 TYR A 696 PHE 0.025 0.002 PHE A 812 TRP 0.011 0.001 TRP A 460 HIS 0.002 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 7793) covalent geometry : angle 0.55018 (10555) SS BOND : bond 0.00076 ( 1) SS BOND : angle 0.08686 ( 2) hydrogen bonds : bond 0.04043 ( 447) hydrogen bonds : angle 4.34224 ( 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 123 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 87 time to evaluate : 0.305 Fit side-chains REVERT: A 29 LEU cc_start: 0.7904 (mt) cc_final: 0.7664 (tp) REVERT: A 85 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6844 (mtt) REVERT: A 100 PHE cc_start: 0.6281 (OUTLIER) cc_final: 0.5734 (t80) REVERT: A 159 ASP cc_start: 0.6399 (OUTLIER) cc_final: 0.5453 (t0) REVERT: A 810 MET cc_start: 0.7839 (mmm) cc_final: 0.7622 (mmm) outliers start: 36 outliers final: 25 residues processed: 112 average time/residue: 0.0777 time to fit residues: 12.5543 Evaluate side-chains 115 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 159 ASP 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 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 611 VAL 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 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: 0.7980 chunk 81 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 95 optimal weight: 30.0000 chunk 31 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 GLN ** 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 = 0.4467 r_free = 0.4467 target = 0.222376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.183969 restraints weight = 7235.544| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 1.94 r_work: 0.3673 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.1560 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= 0.133 Angle : 0.519 7.347 10557 Z= 0.273 Chirality : 0.041 0.329 1248 Planarity : 0.004 0.060 1328 Dihedral : 7.875 117.815 1094 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.02 % Allowed : 18.79 % Favored : 77.19 % 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 aren not related in a simple way. whole: 1.44 (0.27), residues: 989 helix: 1.85 (0.23), residues: 503 sheet: 0.39 (0.42), residues: 134 loop : -0.04 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.009 0.001 TYR A 696 PHE 0.021 0.001 PHE A 812 TRP 0.009 0.001 TRP A 460 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 7793) covalent geometry : angle 0.51896 (10555) SS BOND : bond 0.00085 ( 1) SS BOND : angle 0.14261 ( 2) hydrogen bonds : bond 0.03727 ( 447) hydrogen bonds : angle 4.20726 ( 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 122 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 0.301 Fit side-chains REVERT: A 29 LEU cc_start: 0.7912 (mt) cc_final: 0.7602 (tp) REVERT: A 85 MET cc_start: 0.7291 (mtm) cc_final: 0.7070 (mtt) REVERT: A 100 PHE cc_start: 0.6186 (OUTLIER) cc_final: 0.5617 (t80) REVERT: A 159 ASP cc_start: 0.6364 (OUTLIER) cc_final: 0.5359 (t0) REVERT: A 541 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8200 (mp) outliers start: 34 outliers final: 25 residues processed: 112 average time/residue: 0.0782 time to fit residues: 12.7968 Evaluate side-chains 110 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 88 optimal weight: 40.0000 chunk 46 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4481 r_free = 0.4481 target = 0.224159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.191640 restraints weight = 7205.216| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 1.73 r_work: 0.3760 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 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 0.032 7794 Z= 0.115 Angle : 0.498 8.239 10557 Z= 0.262 Chirality : 0.040 0.300 1248 Planarity : 0.004 0.058 1328 Dihedral : 7.691 116.388 1092 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.73 % Allowed : 18.20 % 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 aren not related in a simple way. whole: 1.62 (0.27), residues: 989 helix: 2.02 (0.23), residues: 503 sheet: 0.58 (0.42), residues: 140 loop : -0.05 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 403 TYR 0.009 0.001 TYR C 127 PHE 0.020 0.001 PHE A 812 TRP 0.007 0.001 TRP A 460 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 7793) covalent geometry : angle 0.49766 (10555) SS BOND : bond 0.00143 ( 1) SS BOND : angle 0.24768 ( 2) hydrogen bonds : bond 0.03508 ( 447) hydrogen bonds : angle 4.05603 ( 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 127 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 87 time to evaluate : 0.295 Fit side-chains REVERT: A 85 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6918 (mtt) REVERT: A 100 PHE cc_start: 0.6238 (OUTLIER) cc_final: 0.5738 (t80) REVERT: A 159 ASP cc_start: 0.6365 (OUTLIER) cc_final: 0.5348 (t0) REVERT: A 541 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8191 (mp) outliers start: 40 outliers final: 30 residues processed: 116 average time/residue: 0.0817 time to fit residues: 13.3236 Evaluate side-chains 116 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 82 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 169 VAL 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 378 VAL 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 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 611 VAL Chi-restraints excluded: chain A residue 682 PHE 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 16 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 36 optimal weight: 0.0770 chunk 96 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.4479 r_free = 0.4479 target = 0.224025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.188596 restraints weight = 7267.627| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 1.73 r_work: 0.3714 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7794 Z= 0.121 Angle : 0.506 8.064 10557 Z= 0.265 Chirality : 0.040 0.279 1248 Planarity : 0.004 0.057 1328 Dihedral : 7.690 116.591 1092 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.02 % Allowed : 19.50 % 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 aren not related in a simple way. whole: 1.61 (0.27), residues: 989 helix: 2.00 (0.23), residues: 503 sheet: 0.59 (0.42), residues: 140 loop : -0.05 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 174 TYR 0.009 0.001 TYR A 696 PHE 0.019 0.001 PHE A 812 TRP 0.012 0.001 TRP A 460 HIS 0.006 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7793) covalent geometry : angle 0.50570 (10555) SS BOND : bond 0.00137 ( 1) SS BOND : angle 0.25238 ( 2) hydrogen bonds : bond 0.03562 ( 447) hydrogen bonds : angle 4.08123 ( 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 114 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 0.306 Fit side-chains REVERT: A 85 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6941 (mtt) REVERT: A 100 PHE cc_start: 0.6233 (OUTLIER) cc_final: 0.5614 (t80) REVERT: A 159 ASP cc_start: 0.6400 (OUTLIER) cc_final: 0.5339 (t0) REVERT: A 541 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8188 (mp) outliers start: 34 outliers final: 29 residues processed: 105 average time/residue: 0.0818 time to fit residues: 12.3595 Evaluate side-chains 111 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 78 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 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 378 VAL 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 541 LEU Chi-restraints excluded: chain A residue 544 ILE 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 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: 20.0000 chunk 80 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 71 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 4 optimal weight: 0.0000 chunk 34 optimal weight: 0.2980 chunk 21 optimal weight: 0.0270 overall best weight: 0.2642 ------------------------------------------------------------------------------- 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 = 0.4493 r_free = 0.4493 target = 0.225805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.187916 restraints weight = 7189.883| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 1.83 r_work: 0.3749 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7794 Z= 0.102 Angle : 0.490 8.450 10557 Z= 0.258 Chirality : 0.040 0.261 1248 Planarity : 0.004 0.054 1328 Dihedral : 7.600 114.129 1092 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.78 % Allowed : 19.86 % 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 aren not related in a simple way. whole: 1.77 (0.27), residues: 989 helix: 2.13 (0.23), residues: 502 sheet: 0.88 (0.44), residues: 134 loop : -0.06 (0.35), residues: 353 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 0.017 0.001 PHE A 812 TRP 0.009 0.001 TRP A 460 HIS 0.001 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 7793) covalent geometry : angle 0.49036 (10555) SS BOND : bond 0.00146 ( 1) SS BOND : angle 0.30806 ( 2) hydrogen bonds : bond 0.03377 ( 447) hydrogen bonds : angle 3.99354 ( 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 117 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.253 Fit side-chains REVERT: A 85 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6875 (mtt) REVERT: A 100 PHE cc_start: 0.6192 (OUTLIER) cc_final: 0.5544 (t80) REVERT: A 149 HIS cc_start: 0.6536 (OUTLIER) cc_final: 0.6300 (p-80) REVERT: A 541 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8193 (mp) outliers start: 32 outliers final: 27 residues processed: 105 average time/residue: 0.0756 time to fit residues: 11.4408 Evaluate side-chains 114 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 149 HIS 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 378 VAL 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 541 LEU Chi-restraints excluded: chain A residue 544 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 74 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.222159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.192926 restraints weight = 7237.242| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 1.81 r_work: 0.3749 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7794 Z= 0.157 Angle : 0.540 8.727 10557 Z= 0.283 Chirality : 0.042 0.264 1248 Planarity : 0.005 0.058 1328 Dihedral : 7.917 118.658 1092 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.02 % Allowed : 19.50 % 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 aren not related in a simple way. whole: 1.52 (0.27), residues: 989 helix: 1.89 (0.23), residues: 502 sheet: 0.77 (0.43), residues: 135 loop : -0.12 (0.35), residues: 352 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 0.024 0.002 PHE A 454 TRP 0.015 0.001 TRP A 460 HIS 0.005 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 7793) covalent geometry : angle 0.53981 (10555) SS BOND : bond 0.00148 ( 1) SS BOND : angle 0.30488 ( 2) hydrogen bonds : bond 0.03786 ( 447) hydrogen bonds : angle 4.18761 ( 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 117 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 0.296 Fit side-chains REVERT: A 85 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6957 (mtt) REVERT: A 100 PHE cc_start: 0.6276 (OUTLIER) cc_final: 0.5666 (t80) REVERT: A 159 ASP cc_start: 0.6402 (OUTLIER) cc_final: 0.5426 (t0) REVERT: A 541 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8223 (mp) outliers start: 34 outliers final: 29 residues processed: 108 average time/residue: 0.0796 time to fit residues: 12.3947 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 : 0.277 ------------------------------------------------------------------------------- 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 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 378 VAL 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 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 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: 0.9980 chunk 44 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.4468 r_free = 0.4468 target = 0.222596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.192426 restraints weight = 7244.691| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 1.62 r_work: 0.3793 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1857 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= 0.136 Angle : 0.525 8.909 10557 Z= 0.276 Chirality : 0.041 0.257 1248 Planarity : 0.004 0.057 1328 Dihedral : 7.887 117.668 1092 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.90 % Allowed : 19.62 % 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 aren not related in a simple way. whole: 1.51 (0.27), residues: 989 helix: 1.88 (0.23), residues: 502 sheet: 0.83 (0.43), residues: 134 loop : -0.15 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 403 TYR 0.009 0.001 TYR A 696 PHE 0.028 0.002 PHE A 812 TRP 0.011 0.001 TRP A 460 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7793) covalent geometry : angle 0.52550 (10555) SS BOND : bond 0.00142 ( 1) SS BOND : angle 0.29478 ( 2) hydrogen bonds : bond 0.03685 ( 447) hydrogen bonds : angle 4.18200 ( 1404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1849.38 seconds wall clock time: 32 minutes 31.71 seconds (1951.71 seconds total)