Starting phenix.real_space_refine on Tue Jan 21 12:48:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r1f_18809/01_2025/8r1f_18809.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r1f_18809/01_2025/8r1f_18809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r1f_18809/01_2025/8r1f_18809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r1f_18809/01_2025/8r1f_18809.map" model { file = "/net/cci-nas-00/data/ceres_data/8r1f_18809/01_2025/8r1f_18809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r1f_18809/01_2025/8r1f_18809.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.059 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 Zn 3 6.06 5 S 56 5.16 5 C 5305 2.51 5 N 1431 2.21 5 O 1571 1.98 5 H 8263 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 16629 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 11110 Classifications: {'peptide': 681} Link IDs: {'PTRANS': 28, 'TRANS': 652} Chain breaks: 1 Chain: "B" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2365 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "C" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3151 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 15, 'TRANS': 186} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12835 SG CYS B 110 56.475 36.607 79.155 1.00176.24 S ATOM 12878 SG CYS B 113 55.532 34.457 81.709 1.00179.11 S ATOM 13405 SG CYS B 143 55.194 38.288 82.316 1.00194.25 S ATOM 13429 SG CYS B 146 58.574 36.731 82.368 1.00210.49 S ATOM 11605 SG CYS B 37 56.648 19.590 79.458 1.00183.23 S ATOM 11652 SG CYS B 40 59.322 17.617 80.885 1.00176.19 S ATOM 12158 SG CYS B 70 58.332 21.223 82.276 1.00180.55 S ATOM 12202 SG CYS B 73 60.186 20.867 79.074 1.00173.90 S ATOM 14814 SG CYS C 176 16.452 40.292 92.297 1.00246.45 S ATOM 15777 SG CYS C 238 18.788 39.517 89.134 1.00228.58 S ATOM 15823 SG CYS C 242 20.345 40.437 92.437 1.00243.62 S Time building chain proxies: 7.66, per 1000 atoms: 0.46 Number of scatterers: 16629 At special positions: 0 Unit cell: (118.44, 109.62, 109.62, 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) Zn 3 29.99 S 56 16.00 O 1571 8.00 N 1431 7.00 C 5305 6.00 H 8263 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.28 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 110 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 113 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 143 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 146 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 37 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 70 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" ND1 HIS C 179 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 238 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 242 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 176 " Number of angles added : 15 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 9 sheets defined 56.4% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 129 through 143 removed outlier: 3.874A pdb=" N ILE A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 159 through 167 removed outlier: 4.206A pdb=" N PHE A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'A' and resid 249 through 274 removed outlier: 3.536A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) Proline residue: A 265 - end of helix removed outlier: 3.535A pdb=" N CYS A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.573A pdb=" N ARG A 279 " --> pdb=" O ASN A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 293 through 297 removed outlier: 3.703A pdb=" N LEU A 296 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N HIS A 297 " --> pdb=" O ARG A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 297' Processing helix chain 'A' and resid 298 through 304 removed outlier: 4.301A pdb=" N MET A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 317 through 329 Processing helix chain 'A' and resid 332 through 354 removed outlier: 3.533A pdb=" N LEU A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 364 Processing helix chain 'A' and resid 365 through 386 Processing helix chain 'A' and resid 403 through 413 Processing helix chain 'A' and resid 426 through 433 Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 451 through 458 Processing helix chain 'A' and resid 459 through 469 Processing helix chain 'A' and resid 476 through 484 Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 485 through 516 Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'A' and resid 549 through 553 Processing helix chain 'A' and resid 568 through 584 Processing helix chain 'A' and resid 585 through 588 Processing helix chain 'A' and resid 608 through 625 removed outlier: 3.982A pdb=" N PHE A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 642 removed outlier: 4.114A pdb=" N TYR A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 650 through 655 removed outlier: 3.815A pdb=" N SER A 654 " --> pdb=" O ASP A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 668 removed outlier: 3.592A pdb=" N SER A 661 " --> pdb=" O VAL A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 709 through 723 Processing helix chain 'A' and resid 726 through 742 removed outlier: 3.684A pdb=" N ALA A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL A 740 " --> pdb=" O GLY A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 Processing helix chain 'A' and resid 751 through 761 removed outlier: 3.656A pdb=" N LEU A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 774 Processing helix chain 'A' and resid 784 through 797 Processing helix chain 'A' and resid 798 through 811 Processing helix chain 'A' and resid 819 through 823 Processing helix chain 'A' and resid 854 through 869 Processing helix chain 'B' and resid 18 through 26 Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 70 through 85 Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 143 through 148 Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.873A pdb=" N TYR C 107 " --> pdb=" O GLN C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 176 through 181 Processing helix chain 'C' and resid 277 through 292 Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 388 removed outlier: 6.553A pdb=" N GLU A 387 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 522 through 527 Processing sheet with id=AA3, first strand: chain 'A' and resid 590 through 593 removed outlier: 3.673A pdb=" N LEU A 598 " --> pdb=" O ASP A 593 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 681 through 685 Processing sheet with id=AA5, first strand: chain 'A' and resid 775 through 777 removed outlier: 6.606A pdb=" N GLU A 775 " --> pdb=" O ILE A 827 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LYS A 829 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ASP A 777 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLY A 831 " --> pdb=" O ASP A 777 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 826 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A 849 " --> pdb=" O ILE A 826 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA A 828 " --> pdb=" O LEU A 849 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLU A 851 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ASN A 830 " --> pdb=" O GLU A 851 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.334A pdb=" N GLU B 36 " --> pdb=" O ALA B 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 86 through 91 removed outlier: 3.780A pdb=" N TYR B 88 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG B 109 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 110 through 113 removed outlier: 4.516A pdb=" N HIS C 233 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 124 through 127 removed outlier: 4.211A pdb=" N ILE C 251 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA C 161 " --> pdb=" O HIS C 214 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N HIS C 214 " --> pdb=" O ALA C 161 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1176 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: 6.19 Time building geometry restraints manager: 5.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 8245 1.03 - 1.23: 29 1.23 - 1.42: 3574 1.42 - 1.62: 4872 1.62 - 1.82: 83 Bond restraints: 16803 Sorted by residual: bond pdb=" N VAL A 234 " pdb=" H VAL A 234 " ideal model delta sigma weight residual 0.860 0.963 -0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" N MET B 8 " pdb=" CA MET B 8 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.42e+00 bond pdb=" CD ARG A 500 " pdb=" NE ARG A 500 " ideal model delta sigma weight residual 1.458 1.429 0.029 1.40e-02 5.10e+03 4.18e+00 bond pdb=" CG ARG A 500 " pdb=" CD ARG A 500 " ideal model delta sigma weight residual 1.520 1.468 0.052 3.00e-02 1.11e+03 3.01e+00 bond pdb=" CA ASP A 389 " pdb=" CB ASP A 389 " ideal model delta sigma weight residual 1.526 1.552 -0.026 1.53e-02 4.27e+03 2.82e+00 ... (remaining 16798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 28886 1.87 - 3.75: 1380 3.75 - 5.62: 63 5.62 - 7.49: 12 7.49 - 9.37: 3 Bond angle restraints: 30344 Sorted by residual: angle pdb=" CB ARG A 500 " pdb=" CG ARG A 500 " pdb=" CD ARG A 500 " ideal model delta sigma weight residual 111.30 101.93 9.37 2.30e+00 1.89e-01 1.66e+01 angle pdb=" C GLU A 135 " pdb=" CA GLU A 135 " pdb=" CB GLU A 135 " ideal model delta sigma weight residual 110.46 103.06 7.40 1.94e+00 2.66e-01 1.46e+01 angle pdb=" C PHE A 256 " pdb=" CA PHE A 256 " pdb=" CB PHE A 256 " ideal model delta sigma weight residual 110.88 105.73 5.15 1.57e+00 4.06e-01 1.07e+01 angle pdb=" CA TYR A 146 " pdb=" CB TYR A 146 " pdb=" CG TYR A 146 " ideal model delta sigma weight residual 113.90 108.05 5.85 1.80e+00 3.09e-01 1.06e+01 angle pdb=" N LEU A 458 " pdb=" CA LEU A 458 " pdb=" C LEU A 458 " ideal model delta sigma weight residual 109.76 114.44 -4.68 1.59e+00 3.96e-01 8.67e+00 ... (remaining 30339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 7143 15.96 - 31.93: 452 31.93 - 47.89: 157 47.89 - 63.85: 133 63.85 - 79.82: 31 Dihedral angle restraints: 7916 sinusoidal: 4351 harmonic: 3565 Sorted by residual: dihedral pdb=" CD ARG A 500 " pdb=" NE ARG A 500 " pdb=" CZ ARG A 500 " pdb=" NH1 ARG A 500 " ideal model delta sinusoidal sigma weight residual 0.00 42.03 -42.03 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CA SER B 147 " pdb=" C SER B 147 " pdb=" N ARG B 148 " pdb=" CA ARG B 148 " ideal model delta harmonic sigma weight residual 180.00 160.95 19.05 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" C ASN A 699 " pdb=" N ASN A 699 " pdb=" CA ASN A 699 " pdb=" CB ASN A 699 " ideal model delta harmonic sigma weight residual -122.60 -131.47 8.87 0 2.50e+00 1.60e-01 1.26e+01 ... (remaining 7913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 768 0.056 - 0.111: 353 0.111 - 0.167: 117 0.167 - 0.222: 18 0.222 - 0.278: 4 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA ASN A 699 " pdb=" N ASN A 699 " pdb=" C ASN A 699 " pdb=" CB ASN A 699 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ILE B 34 " pdb=" N ILE B 34 " pdb=" C ILE B 34 " pdb=" CB ILE B 34 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ARG C 248 " pdb=" N ARG C 248 " pdb=" C ARG C 248 " pdb=" CB ARG C 248 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1257 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 500 " 0.874 9.50e-02 1.11e+02 2.92e-01 9.43e+01 pdb=" NE ARG A 500 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 500 " -0.052 2.00e-02 2.50e+03 pdb=" NH1 ARG A 500 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 500 " 0.008 2.00e-02 2.50e+03 pdb="HH11 ARG A 500 " -0.008 2.00e-02 2.50e+03 pdb="HH12 ARG A 500 " 0.008 2.00e-02 2.50e+03 pdb="HH21 ARG A 500 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 500 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 734 " -0.426 9.50e-02 1.11e+02 1.42e-01 2.16e+01 pdb=" NE ARG A 734 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 734 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 734 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 734 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 734 " 0.009 2.00e-02 2.50e+03 pdb="HH12 ARG A 734 " -0.004 2.00e-02 2.50e+03 pdb="HH21 ARG A 734 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 734 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 256 " -0.045 2.00e-02 2.50e+03 1.95e-02 1.14e+01 pdb=" CG PHE A 256 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 256 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 256 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 256 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 256 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 256 " -0.008 2.00e-02 2.50e+03 pdb=" HD1 PHE A 256 " 0.007 2.00e-02 2.50e+03 pdb=" HD2 PHE A 256 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 PHE A 256 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 256 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 256 " -0.007 2.00e-02 2.50e+03 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 1706 2.26 - 2.85: 38212 2.85 - 3.43: 42591 3.43 - 4.02: 58195 4.02 - 4.60: 90108 Nonbonded interactions: 230812 Sorted by model distance: nonbonded pdb=" OE2 GLU A 130 " pdb=" HH TYR A 134 " model vdw 1.677 2.450 nonbonded pdb=" O PRO C 152 " pdb=" HG1 THR C 155 " model vdw 1.693 2.450 nonbonded pdb=" HH TYR A 668 " pdb=" OD2 ASP A 675 " model vdw 1.703 2.450 nonbonded pdb=" O PRO B 16 " pdb=" HH TYR B 61 " model vdw 1.708 2.450 nonbonded pdb=" HG SER C 95 " pdb=" O THR C 211 " model vdw 1.726 2.450 ... (remaining 230807 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.270 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 43.250 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5340 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 : 0.008 0.053 8540 Z= 0.483 Angle : 0.979 9.367 11541 Z= 0.572 Chirality : 0.068 0.278 1260 Planarity : 0.016 0.377 1501 Dihedral : 11.490 79.816 3271 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 0.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.21 % Allowed : 2.66 % Favored : 97.12 % 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: -0.70 (0.25), residues: 1017 helix: -0.82 (0.20), residues: 482 sheet: -0.21 (0.47), residues: 118 loop : 0.21 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP A 791 HIS 0.013 0.003 HIS C 233 PHE 0.051 0.005 PHE A 256 TYR 0.030 0.004 TYR A 494 ARG 0.037 0.001 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 254 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 GLU cc_start: 0.6539 (tt0) cc_final: 0.6319 (tp30) REVERT: A 313 MET cc_start: 0.7243 (ttm) cc_final: 0.6893 (ttm) REVERT: A 389 ASP cc_start: 0.6868 (m-30) cc_final: 0.5336 (p0) REVERT: A 415 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6837 (mp0) REVERT: A 470 GLU cc_start: 0.5170 (tt0) cc_final: 0.4952 (mm-30) REVERT: A 556 TYR cc_start: 0.7071 (t80) cc_final: 0.6333 (t80) REVERT: A 558 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6402 (mm-30) REVERT: A 559 PHE cc_start: 0.6303 (m-80) cc_final: 0.6009 (m-80) REVERT: A 591 THR cc_start: 0.5311 (p) cc_final: 0.4542 (m) REVERT: A 630 ASP cc_start: 0.6216 (p0) cc_final: 0.5757 (p0) REVERT: A 756 GLU cc_start: 0.6405 (tt0) cc_final: 0.6122 (tm-30) REVERT: A 757 LEU cc_start: 0.6630 (mt) cc_final: 0.6278 (tt) REVERT: B 47 ARG cc_start: 0.7264 (tpp80) cc_final: 0.7057 (tpp80) REVERT: B 58 CYS cc_start: 0.7062 (m) cc_final: 0.6222 (t) REVERT: B 61 TYR cc_start: 0.6486 (m-80) cc_final: 0.5270 (m-80) REVERT: B 72 LYS cc_start: 0.9120 (pttm) cc_final: 0.8878 (pttm) REVERT: B 90 LEU cc_start: 0.4983 (mt) cc_final: 0.4625 (mp) REVERT: B 129 LYS cc_start: 0.7730 (mttt) cc_final: 0.6998 (mmmt) REVERT: C 100 GLN cc_start: 0.7958 (pt0) cc_final: 0.7682 (pt0) REVERT: C 137 LEU cc_start: 0.7216 (tp) cc_final: 0.6625 (tp) REVERT: C 163 TYR cc_start: 0.4948 (m-80) cc_final: 0.4259 (m-80) REVERT: C 165 GLN cc_start: 0.8806 (mt0) cc_final: 0.8296 (mt0) REVERT: C 196 ARG cc_start: 0.7032 (mtt180) cc_final: 0.6282 (ttp-110) REVERT: C 271 GLU cc_start: 0.7220 (tt0) cc_final: 0.6909 (tt0) outliers start: 2 outliers final: 1 residues processed: 256 average time/residue: 0.6112 time to fit residues: 202.7880 Evaluate side-chains 159 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 209 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 0.0980 chunk 26 optimal weight: 0.0970 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.223821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.187591 restraints weight = 38955.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.194511 restraints weight = 19682.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.198850 restraints weight = 12720.540| |-----------------------------------------------------------------------------| r_work (final): 0.4497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8540 Z= 0.192 Angle : 0.587 5.222 11541 Z= 0.312 Chirality : 0.040 0.140 1260 Planarity : 0.005 0.046 1501 Dihedral : 4.699 56.088 1146 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.17 % Allowed : 8.09 % Favored : 90.73 % 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: 0.62 (0.26), residues: 1017 helix: 0.75 (0.23), residues: 484 sheet: -0.12 (0.47), residues: 120 loop : 0.39 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 791 HIS 0.006 0.001 HIS C 168 PHE 0.019 0.002 PHE A 730 TYR 0.016 0.002 TYR A 624 ARG 0.008 0.001 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ILE cc_start: 0.7105 (mm) cc_final: 0.6753 (mt) REVERT: A 511 TYR cc_start: 0.7261 (OUTLIER) cc_final: 0.6686 (t80) REVERT: A 556 TYR cc_start: 0.6371 (t80) cc_final: 0.6040 (t80) REVERT: A 559 PHE cc_start: 0.7532 (m-80) cc_final: 0.7262 (m-80) REVERT: A 591 THR cc_start: 0.7486 (p) cc_final: 0.6124 (m) REVERT: A 757 LEU cc_start: 0.8490 (mt) cc_final: 0.7826 (tt) REVERT: B 18 LYS cc_start: 0.7848 (mmtt) cc_final: 0.7537 (mmmt) REVERT: B 58 CYS cc_start: 0.7946 (m) cc_final: 0.7355 (t) REVERT: B 127 ASP cc_start: 0.7116 (m-30) cc_final: 0.6874 (m-30) REVERT: C 287 GLU cc_start: 0.7353 (pt0) cc_final: 0.7140 (pt0) outliers start: 11 outliers final: 8 residues processed: 166 average time/residue: 0.5181 time to fit residues: 114.7271 Evaluate side-chains 141 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 289 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.219121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.185137 restraints weight = 38584.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.191946 restraints weight = 21230.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.194239 restraints weight = 12610.211| |-----------------------------------------------------------------------------| r_work (final): 0.4457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8540 Z= 0.240 Angle : 0.565 4.966 11541 Z= 0.301 Chirality : 0.039 0.147 1260 Planarity : 0.005 0.052 1501 Dihedral : 4.674 57.969 1146 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.70 % Allowed : 10.12 % Favored : 88.18 % 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: 0.67 (0.26), residues: 1017 helix: 0.80 (0.23), residues: 487 sheet: -0.29 (0.47), residues: 120 loop : 0.47 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 791 HIS 0.005 0.001 HIS C 168 PHE 0.022 0.002 PHE A 467 TYR 0.019 0.002 TYR B 86 ARG 0.006 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 511 TYR cc_start: 0.7355 (OUTLIER) cc_final: 0.6674 (t80) REVERT: A 556 TYR cc_start: 0.6176 (t80) cc_final: 0.5888 (t80) REVERT: A 591 THR cc_start: 0.7595 (p) cc_final: 0.6019 (m) REVERT: A 757 LEU cc_start: 0.8531 (mt) cc_final: 0.7916 (tt) REVERT: B 58 CYS cc_start: 0.7899 (m) cc_final: 0.7147 (t) REVERT: B 127 ASP cc_start: 0.6861 (m-30) cc_final: 0.6518 (m-30) REVERT: C 160 MET cc_start: 0.7277 (ttp) cc_final: 0.7060 (ttp) REVERT: C 206 LEU cc_start: 0.4684 (mp) cc_final: 0.3973 (tt) outliers start: 16 outliers final: 10 residues processed: 148 average time/residue: 0.5167 time to fit residues: 102.9196 Evaluate side-chains 130 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 289 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 0.0000 chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.217972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.184190 restraints weight = 38364.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.191176 restraints weight = 20418.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.193281 restraints weight = 12093.272| |-----------------------------------------------------------------------------| r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8540 Z= 0.187 Angle : 0.522 5.004 11541 Z= 0.274 Chirality : 0.038 0.136 1260 Planarity : 0.004 0.043 1501 Dihedral : 4.539 58.867 1146 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.92 % Allowed : 10.86 % Favored : 87.22 % 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: 0.88 (0.27), residues: 1017 helix: 0.98 (0.23), residues: 487 sheet: -0.26 (0.48), residues: 116 loop : 0.60 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 139 HIS 0.003 0.001 HIS C 233 PHE 0.016 0.002 PHE A 467 TYR 0.016 0.001 TYR C 107 ARG 0.005 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 511 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.6603 (t80) REVERT: A 591 THR cc_start: 0.7587 (p) cc_final: 0.5988 (m) REVERT: A 757 LEU cc_start: 0.8560 (mt) cc_final: 0.7947 (tt) REVERT: B 58 CYS cc_start: 0.7910 (m) cc_final: 0.7242 (t) REVERT: B 127 ASP cc_start: 0.6732 (m-30) cc_final: 0.6391 (m-30) REVERT: C 140 THR cc_start: 0.6295 (OUTLIER) cc_final: 0.5798 (t) REVERT: C 206 LEU cc_start: 0.4624 (mp) cc_final: 0.3896 (tt) outliers start: 18 outliers final: 14 residues processed: 138 average time/residue: 0.5072 time to fit residues: 95.0228 Evaluate side-chains 132 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 289 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 68 optimal weight: 0.0010 chunk 24 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.218421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.184783 restraints weight = 38744.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.191187 restraints weight = 20995.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.193502 restraints weight = 12779.173| |-----------------------------------------------------------------------------| r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8540 Z= 0.167 Angle : 0.505 6.316 11541 Z= 0.261 Chirality : 0.038 0.162 1260 Planarity : 0.004 0.041 1501 Dihedral : 4.388 59.436 1146 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.13 % Allowed : 10.86 % Favored : 87.01 % 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: 1.11 (0.27), residues: 1017 helix: 1.21 (0.23), residues: 487 sheet: -0.22 (0.48), residues: 116 loop : 0.66 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 139 HIS 0.002 0.001 HIS A 392 PHE 0.014 0.001 PHE A 730 TYR 0.013 0.001 TYR B 86 ARG 0.004 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 MET cc_start: 0.8308 (mmm) cc_final: 0.7524 (tpt) REVERT: A 470 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.5341 (mp0) REVERT: A 511 TYR cc_start: 0.7310 (OUTLIER) cc_final: 0.6578 (t80) REVERT: A 591 THR cc_start: 0.7564 (p) cc_final: 0.5961 (m) REVERT: A 757 LEU cc_start: 0.8438 (mt) cc_final: 0.7947 (tt) REVERT: B 18 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7569 (mmmt) REVERT: B 58 CYS cc_start: 0.7962 (m) cc_final: 0.7243 (t) REVERT: C 200 ASN cc_start: 0.7023 (m110) cc_final: 0.6799 (m-40) REVERT: C 206 LEU cc_start: 0.4379 (mp) cc_final: 0.3650 (tt) outliers start: 20 outliers final: 13 residues processed: 139 average time/residue: 0.5196 time to fit residues: 96.6161 Evaluate side-chains 134 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 289 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 31 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.214297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.178742 restraints weight = 38366.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.182873 restraints weight = 22703.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.185799 restraints weight = 14864.004| |-----------------------------------------------------------------------------| r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8540 Z= 0.248 Angle : 0.542 5.325 11541 Z= 0.285 Chirality : 0.039 0.135 1260 Planarity : 0.005 0.051 1501 Dihedral : 4.559 59.614 1146 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.92 % Allowed : 11.61 % Favored : 86.47 % 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: 0.84 (0.26), residues: 1017 helix: 0.99 (0.23), residues: 487 sheet: -0.35 (0.49), residues: 116 loop : 0.53 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 139 HIS 0.004 0.001 HIS A 392 PHE 0.025 0.002 PHE A 467 TYR 0.020 0.002 TYR B 86 ARG 0.004 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7429 (mm-30) REVERT: A 470 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.5469 (mp0) REVERT: A 511 TYR cc_start: 0.7335 (OUTLIER) cc_final: 0.6560 (t80) REVERT: A 537 LEU cc_start: 0.5158 (tt) cc_final: 0.4831 (tt) REVERT: A 552 LYS cc_start: 0.7690 (mttp) cc_final: 0.7468 (mmtm) REVERT: A 591 THR cc_start: 0.7548 (p) cc_final: 0.6004 (m) REVERT: A 757 LEU cc_start: 0.8480 (mt) cc_final: 0.7966 (tt) REVERT: B 58 CYS cc_start: 0.7968 (m) cc_final: 0.7211 (t) REVERT: C 200 ASN cc_start: 0.7081 (m110) cc_final: 0.6821 (m-40) REVERT: C 206 LEU cc_start: 0.4487 (mp) cc_final: 0.3604 (tt) outliers start: 18 outliers final: 15 residues processed: 134 average time/residue: 0.4778 time to fit residues: 88.1978 Evaluate side-chains 137 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 289 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 93 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.212464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.177476 restraints weight = 38101.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.183980 restraints weight = 20984.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.185465 restraints weight = 13263.414| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8540 Z= 0.277 Angle : 0.567 7.092 11541 Z= 0.299 Chirality : 0.040 0.142 1260 Planarity : 0.005 0.055 1501 Dihedral : 4.698 59.519 1146 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.45 % Allowed : 11.93 % Favored : 85.62 % 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: 0.60 (0.26), residues: 1017 helix: 0.81 (0.23), residues: 481 sheet: -0.48 (0.50), residues: 113 loop : 0.39 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 139 HIS 0.006 0.001 HIS A 392 PHE 0.025 0.002 PHE A 467 TYR 0.018 0.002 TYR B 86 ARG 0.005 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.5473 (mp0) REVERT: A 511 TYR cc_start: 0.7391 (OUTLIER) cc_final: 0.6561 (t80) REVERT: A 537 LEU cc_start: 0.5430 (tt) cc_final: 0.5106 (tt) REVERT: A 757 LEU cc_start: 0.8496 (mt) cc_final: 0.7994 (tt) REVERT: A 825 MET cc_start: 0.0067 (ttm) cc_final: -0.0174 (ttm) REVERT: B 58 CYS cc_start: 0.8066 (m) cc_final: 0.7236 (t) REVERT: C 200 ASN cc_start: 0.7114 (m110) cc_final: 0.6873 (m-40) REVERT: C 206 LEU cc_start: 0.4339 (mp) cc_final: 0.3533 (tt) outliers start: 23 outliers final: 17 residues processed: 131 average time/residue: 0.4865 time to fit residues: 86.8424 Evaluate side-chains 138 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 289 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 68 optimal weight: 0.0370 chunk 31 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 55 optimal weight: 0.0170 chunk 71 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN C 193 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.215519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.181041 restraints weight = 38134.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.185492 restraints weight = 21361.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.188800 restraints weight = 14406.132| |-----------------------------------------------------------------------------| r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8540 Z= 0.157 Angle : 0.503 7.770 11541 Z= 0.260 Chirality : 0.038 0.138 1260 Planarity : 0.004 0.046 1501 Dihedral : 4.433 59.975 1146 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.38 % Allowed : 13.10 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.27), residues: 1017 helix: 1.22 (0.24), residues: 480 sheet: -0.24 (0.51), residues: 111 loop : 0.53 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 139 HIS 0.005 0.001 HIS C 193 PHE 0.014 0.001 PHE A 730 TYR 0.020 0.001 TYR C 103 ARG 0.004 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.5126 (mp0) REVERT: A 511 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.6442 (t80) REVERT: B 58 CYS cc_start: 0.8086 (m) cc_final: 0.7237 (t) REVERT: C 200 ASN cc_start: 0.7241 (m110) cc_final: 0.6933 (m-40) REVERT: C 206 LEU cc_start: 0.4198 (mp) cc_final: 0.3408 (tt) outliers start: 13 outliers final: 9 residues processed: 122 average time/residue: 0.5036 time to fit residues: 83.6112 Evaluate side-chains 125 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 209 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 0.0670 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 50 optimal weight: 0.0070 chunk 76 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.215816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.181207 restraints weight = 38238.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.185423 restraints weight = 21423.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.188479 restraints weight = 14644.590| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.5806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8540 Z= 0.158 Angle : 0.507 8.278 11541 Z= 0.260 Chirality : 0.038 0.140 1260 Planarity : 0.004 0.041 1501 Dihedral : 4.315 59.991 1146 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.17 % Allowed : 13.63 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.27), residues: 1017 helix: 1.39 (0.24), residues: 481 sheet: -0.15 (0.51), residues: 111 loop : 0.63 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 139 HIS 0.003 0.001 HIS A 392 PHE 0.014 0.001 PHE A 612 TYR 0.018 0.001 TYR C 103 ARG 0.003 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.5383 (mp0) REVERT: A 511 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.6452 (t80) REVERT: A 591 THR cc_start: 0.7342 (p) cc_final: 0.5901 (m) REVERT: B 58 CYS cc_start: 0.8086 (m) cc_final: 0.7280 (t) REVERT: C 200 ASN cc_start: 0.7143 (m110) cc_final: 0.6827 (m-40) REVERT: C 206 LEU cc_start: 0.4196 (mp) cc_final: 0.3402 (tt) outliers start: 11 outliers final: 8 residues processed: 125 average time/residue: 0.4591 time to fit residues: 79.1834 Evaluate side-chains 124 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 209 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 89 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.213137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.178429 restraints weight = 37890.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.182489 restraints weight = 22608.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.184895 restraints weight = 15071.746| |-----------------------------------------------------------------------------| r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8540 Z= 0.246 Angle : 0.551 7.931 11541 Z= 0.288 Chirality : 0.039 0.140 1260 Planarity : 0.005 0.047 1501 Dihedral : 4.497 59.756 1146 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.17 % Allowed : 13.31 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1017 helix: 1.08 (0.23), residues: 481 sheet: -0.37 (0.50), residues: 115 loop : 0.46 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 139 HIS 0.004 0.001 HIS A 392 PHE 0.022 0.002 PHE A 467 TYR 0.019 0.001 TYR B 86 ARG 0.004 0.000 ARG A 500 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.5501 (mp0) REVERT: A 511 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.6550 (t80) REVERT: A 537 LEU cc_start: 0.5207 (tt) cc_final: 0.4846 (tt) REVERT: B 58 CYS cc_start: 0.8061 (m) cc_final: 0.7240 (t) REVERT: C 200 ASN cc_start: 0.7316 (m110) cc_final: 0.6895 (m-40) REVERT: C 206 LEU cc_start: 0.4244 (mp) cc_final: 0.3451 (tt) outliers start: 11 outliers final: 8 residues processed: 123 average time/residue: 0.4883 time to fit residues: 83.5090 Evaluate side-chains 124 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 209 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 81 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 39 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 65 optimal weight: 0.0060 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.215963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.181585 restraints weight = 38020.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.187084 restraints weight = 20600.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.189565 restraints weight = 13209.234| |-----------------------------------------------------------------------------| r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.6017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8540 Z= 0.155 Angle : 0.502 8.926 11541 Z= 0.261 Chirality : 0.038 0.139 1260 Planarity : 0.004 0.042 1501 Dihedral : 4.291 59.905 1146 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.28 % Allowed : 13.53 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.27 (0.27), residues: 1017 helix: 1.50 (0.24), residues: 474 sheet: -0.20 (0.51), residues: 111 loop : 0.57 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 139 HIS 0.003 0.001 HIS A 392 PHE 0.014 0.001 PHE A 612 TYR 0.018 0.001 TYR C 103 ARG 0.003 0.000 ARG A 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5297.50 seconds wall clock time: 94 minutes 29.86 seconds (5669.86 seconds total)