Starting phenix.real_space_refine on Thu Aug 6 10:20:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dj8_46936/08_2026/9dj8_46936_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dj8_46936/08_2026/9dj8_46936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dj8_46936/08_2026/9dj8_46936_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dj8_46936/08_2026/9dj8_46936_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dj8_46936/08_2026/9dj8_46936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dj8_46936/08_2026/9dj8_46936.map" } resolution = 2.58 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= -0.001 sd= 0.031 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1 5.49 5 S 54 5.16 5 C 4826 2.51 5 N 1270 2.21 5 O 1416 1.98 5 H 7277 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14846 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 14720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 931, 14720 Classifications: {'peptide': 931} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 900} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 102 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "A" 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: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'AMP%rna3p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna3p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4821 SG CYS A 301 17.273 35.922 70.950 1.00 1.26 S ATOM 4898 SG CYS A 306 16.341 38.172 73.836 1.00 6.08 S ATOM 4963 SG CYS A 310 19.135 34.916 74.170 1.00 2.03 S ATOM 7720 SG CYS A 487 14.817 48.119 53.359 1.00 8.37 S ATOM 10237 SG CYS A 645 13.344 50.103 56.321 1.00 7.07 S ATOM 10247 SG CYS A 646 13.475 46.185 56.417 1.00 6.84 S Time building chain proxies: 2.71, per 1000 atoms: 0.18 Number of scatterers: 14846 At special positions: 0 Unit cell: (84.48, 96, 137.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 54 16.00 P 1 15.00 O 1416 8.00 N 1270 7.00 C 4826 6.00 H 7277 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 567.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " Number of angles added : 6 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1786 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 9 sheets defined 50.0% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.866A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.676A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.605A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.850A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 248 removed outlier: 3.556A pdb=" N LEU A 241 " --> pdb=" O TYR A 237 " (cutoff:3.500A) Proline residue: A 243 - end of helix removed outlier: 4.151A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.646A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.775A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.566A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 removed outlier: 3.509A pdb=" N TYR A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 3.779A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.827A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.993A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.673A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 627 through 639 removed outlier: 3.532A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.662A pdb=" N ILE A 715 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 removed outlier: 3.519A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 removed outlier: 3.539A pdb=" N GLN A 773 " --> pdb=" O THR A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.536A pdb=" N TYR A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.510A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 855 Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 902 removed outlier: 3.997A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 900 " --> pdb=" O THR A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 917 removed outlier: 3.792A pdb=" N GLU A 917 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 removed outlier: 3.547A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.401A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS A 98 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.387A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 331 removed outlier: 6.665A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 338 through 339 removed outlier: 6.686A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 386 through 387 removed outlier: 6.488A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 672 " --> pdb=" O CYS A 669 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA8, first strand: chain 'A' and resid 753 through 757 Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.824A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 891 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.90 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7254 1.03 - 1.23: 113 1.23 - 1.42: 3330 1.42 - 1.62: 4259 1.62 - 1.82: 79 Bond restraints: 15035 Sorted by residual: bond pdb=" C4 AMP G 201 " pdb=" C5 AMP G 201 " ideal model delta sigma weight residual 1.490 1.385 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" C GLY A 203 " pdb=" O GLY A 203 " ideal model delta sigma weight residual 1.236 1.184 0.052 1.12e-02 7.97e+03 2.12e+01 bond pdb=" C5 AMP G 201 " pdb=" C6 AMP G 201 " ideal model delta sigma weight residual 1.490 1.403 0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C LEU A 205 " pdb=" O LEU A 205 " ideal model delta sigma weight residual 1.236 1.196 0.039 1.22e-02 6.72e+03 1.05e+01 bond pdb=" C ASP A 825 " pdb=" O ASP A 825 " ideal model delta sigma weight residual 1.235 1.198 0.037 1.22e-02 6.72e+03 9.29e+00 ... (remaining 15030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.27: 26980 14.27 - 28.54: 3 28.54 - 42.81: 1 42.81 - 57.08: 0 57.08 - 71.36: 1 Bond angle restraints: 26985 Sorted by residual: angle pdb=" C SER A 759 " pdb=" N ASP A 760 " pdb=" CA ASP A 760 " ideal model delta sigma weight residual 122.36 162.98 -40.62 1.42e+00 4.96e-01 8.18e+02 angle pdb=" C SER A 759 " pdb=" N ASP A 760 " pdb=" H ASP A 760 " ideal model delta sigma weight residual 123.97 52.61 71.36 3.00e+00 1.11e-01 5.66e+02 angle pdb=" N ASP A 760 " pdb=" CA ASP A 760 " pdb=" CB ASP A 760 " ideal model delta sigma weight residual 111.70 89.70 22.00 1.48e+00 4.57e-01 2.21e+02 angle pdb=" C SER A 759 " pdb=" CA SER A 759 " pdb=" CB SER A 759 " ideal model delta sigma weight residual 112.06 95.53 16.53 1.57e+00 4.06e-01 1.11e+02 angle pdb=" N SER A 759 " pdb=" CA SER A 759 " pdb=" C SER A 759 " ideal model delta sigma weight residual 111.17 124.57 -13.40 1.41e+00 5.03e-01 9.04e+01 ... (remaining 26980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.80: 6984 31.80 - 63.61: 177 63.61 - 95.41: 10 95.41 - 127.22: 0 127.22 - 159.02: 1 Dihedral angle restraints: 7172 sinusoidal: 3740 harmonic: 3432 Sorted by residual: dihedral pdb=" N ASP A 760 " pdb=" C ASP A 760 " pdb=" CA ASP A 760 " pdb=" CB ASP A 760 " ideal model delta harmonic sigma weight residual 122.80 95.41 27.39 0 2.50e+00 1.60e-01 1.20e+02 dihedral pdb=" C2' AMP G 201 " pdb=" C1' AMP G 201 " pdb=" N9 AMP G 201 " pdb=" C4 AMP G 201 " ideal model delta sinusoidal sigma weight residual 91.55 -67.47 159.02 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" C ASP A 760 " pdb=" N ASP A 760 " pdb=" CA ASP A 760 " pdb=" CB ASP A 760 " ideal model delta harmonic sigma weight residual -122.60 -107.31 -15.29 0 2.50e+00 1.60e-01 3.74e+01 ... (remaining 7169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1127 0.121 - 0.242: 21 0.242 - 0.362: 0 0.362 - 0.483: 1 0.483 - 0.604: 1 Chirality restraints: 1150 Sorted by residual: chirality pdb=" CA ASP A 760 " pdb=" N ASP A 760 " pdb=" C ASP A 760 " pdb=" CB ASP A 760 " both_signs ideal model delta sigma weight residual False 2.51 3.11 -0.60 2.00e-01 2.50e+01 9.12e+00 chirality pdb=" CA VAL A 844 " pdb=" N VAL A 844 " pdb=" C VAL A 844 " pdb=" CB VAL A 844 " both_signs ideal model delta sigma weight residual False 2.44 2.82 -0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA THR A 76 " pdb=" N THR A 76 " pdb=" C THR A 76 " pdb=" CB THR A 76 " both_signs ideal model delta sigma weight residual False 2.53 2.76 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1147 not shown) Planarity restraints: 2259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 74 " -0.210 9.50e-02 1.11e+02 3.35e-01 2.43e+03 pdb=" NE ARG A 74 " 0.244 2.00e-02 2.50e+03 pdb=" CZ ARG A 74 " 0.061 2.00e-02 2.50e+03 pdb=" NH1 ARG A 74 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 74 " -0.046 2.00e-02 2.50e+03 pdb="HH11 ARG A 74 " -0.700 2.00e-02 2.50e+03 pdb="HH12 ARG A 74 " 0.625 2.00e-02 2.50e+03 pdb="HH21 ARG A 74 " -0.146 2.00e-02 2.50e+03 pdb="HH22 ARG A 74 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 822 " -0.230 2.00e-02 2.50e+03 2.76e-01 1.14e+03 pdb=" CD GLN A 822 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN A 822 " 0.228 2.00e-02 2.50e+03 pdb=" NE2 GLN A 822 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 822 " -0.422 2.00e-02 2.50e+03 pdb="HE22 GLN A 822 " 0.417 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 76 " -0.044 2.00e-02 2.50e+03 8.35e-02 6.97e+01 pdb=" N PHE A 77 " 0.144 2.00e-02 2.50e+03 pdb=" CA PHE A 77 " -0.038 2.00e-02 2.50e+03 pdb=" H PHE A 77 " -0.062 2.00e-02 2.50e+03 ... (remaining 2256 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.79: 20 1.79 - 2.49: 9798 2.49 - 3.20: 41618 3.20 - 3.90: 56040 3.90 - 4.60: 89220 Nonbonded interactions: 196696 Sorted by model distance: nonbonded pdb=" O ASP A 845 " pdb="HG12 VAL A 848 " model vdw 1.089 2.620 nonbonded pdb=" O SER A 759 " pdb=" HG SER A 759 " model vdw 1.160 2.450 nonbonded pdb=" O SER A 759 " pdb=" H ASP A 760 " model vdw 1.485 1.960 nonbonded pdb="HH12 ARG A 18 " pdb=" OD1 ASP A 63 " model vdw 1.486 2.450 nonbonded pdb=" OD1 ASP A 846 " pdb=" H ILE A 847 " model vdw 1.520 2.450 ... (remaining 196691 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: 7.300 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: 0.090 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 20.030 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 : 0.007 0.253 7767 Z= 0.310 Angle : 0.930 40.615 10539 Z= 0.566 Chirality : 0.052 0.604 1150 Planarity : 0.009 0.239 1354 Dihedral : 14.203 159.019 2783 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.66 % Allowed : 7.97 % Favored : 89.37 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.25), residues: 934 helix: -0.64 (0.25), residues: 399 sheet: -0.97 (0.42), residues: 124 loop : -1.98 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 654 TYR 0.019 0.003 TYR A 80 PHE 0.025 0.002 PHE A 652 TRP 0.013 0.002 TRP A 916 HIS 0.004 0.001 HIS A 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.29 ( 7758) covalent geometry : angle 0.91221 / 0.56 (10533) hydrogen bonds : bond 0.23607 / 16.08 ( 329) hydrogen bonds : angle 6.37272 / 4.40 ( 891) metal coordination : bond 0.10552 / 5.61 ( 8) metal coordination : angle 7.69042 / 4.66 ( 6) Misc. bond : bond 0.05180 / 2.47 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 849 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 5 residues processed: 65 average time/residue: 1.2626 time to fit residues: 87.2098 Evaluate side-chains 42 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 760 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.054355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.042503 restraints weight = 60220.412| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 2.54 r_work: 0.2600 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7767 Z= 0.154 Angle : 0.540 12.441 10539 Z= 0.303 Chirality : 0.041 0.140 1150 Planarity : 0.004 0.047 1354 Dihedral : 7.644 154.843 1053 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.69 % Allowed : 9.42 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.26), residues: 934 helix: 0.56 (0.27), residues: 395 sheet: -0.51 (0.45), residues: 116 loop : -1.84 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 365 TYR 0.013 0.001 TYR A 80 PHE 0.014 0.001 PHE A 753 TRP 0.012 0.001 TRP A 916 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 7758) covalent geometry : angle 0.53867 / 0.30 (10533) hydrogen bonds : bond 0.06180 / 4.05 ( 329) hydrogen bonds : angle 4.35725 / 3.06 ( 891) metal coordination : bond 0.00664 / 0.34 ( 8) metal coordination : angle 1.39347 / 0.65 ( 6) Misc. bond : bond 0.00011 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 849 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.464 Fit side-chains REVERT: A 681 SER cc_start: 0.9042 (OUTLIER) cc_final: 0.8547 (t) REVERT: A 902 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8055 (ptp) outliers start: 14 outliers final: 7 residues processed: 50 average time/residue: 0.9945 time to fit residues: 53.9501 Evaluate side-chains 45 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 902 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 32 optimal weight: 0.9980 chunk 90 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.055081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.043264 restraints weight = 59994.169| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 2.54 r_work: 0.2627 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7767 Z= 0.120 Angle : 0.488 12.199 10539 Z= 0.271 Chirality : 0.040 0.138 1150 Planarity : 0.004 0.044 1354 Dihedral : 7.207 152.762 1050 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.45 % Allowed : 9.90 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.27), residues: 934 helix: 0.98 (0.27), residues: 400 sheet: -0.30 (0.47), residues: 116 loop : -1.78 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 365 TYR 0.012 0.001 TYR A 80 PHE 0.011 0.001 PHE A 741 TRP 0.012 0.001 TRP A 916 HIS 0.002 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 7758) covalent geometry : angle 0.48748 / 0.27 (10533) hydrogen bonds : bond 0.05020 / 3.28 ( 329) hydrogen bonds : angle 3.99967 / 2.83 ( 891) metal coordination : bond 0.00787 / 0.39 ( 8) metal coordination : angle 1.26818 / 0.59 ( 6) Misc. bond : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 849 is missing expected H atoms. Skipping. Evaluate side-chains 48 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 902 MET cc_start: 0.8004 (ptt) cc_final: 0.7741 (ptp) outliers start: 12 outliers final: 7 residues processed: 46 average time/residue: 1.1104 time to fit residues: 54.9508 Evaluate side-chains 41 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 760 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 70 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 77 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.055466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.043724 restraints weight = 59513.489| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.53 r_work: 0.2644 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7767 Z= 0.111 Angle : 0.468 12.133 10539 Z= 0.259 Chirality : 0.039 0.136 1150 Planarity : 0.004 0.042 1354 Dihedral : 6.974 151.192 1049 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.21 % Allowed : 9.66 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.27), residues: 934 helix: 1.26 (0.28), residues: 400 sheet: -0.30 (0.45), residues: 116 loop : -1.69 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 365 TYR 0.011 0.001 TYR A 80 PHE 0.011 0.001 PHE A 753 TRP 0.012 0.001 TRP A 916 HIS 0.002 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 7758) covalent geometry : angle 0.46767 / 0.26 (10533) hydrogen bonds : bond 0.04515 / 2.94 ( 329) hydrogen bonds : angle 3.85627 / 2.75 ( 891) metal coordination : bond 0.00634 / 0.31 ( 8) metal coordination : angle 1.13060 / 0.52 ( 6) Misc. bond : bond 0.00029 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 849 is missing expected H atoms. Skipping. Evaluate side-chains 46 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 902 MET cc_start: 0.7852 (ptt) cc_final: 0.7590 (ptp) outliers start: 10 outliers final: 6 residues processed: 45 average time/residue: 1.0616 time to fit residues: 51.4795 Evaluate side-chains 42 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 760 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 70 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 72 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 chunk 58 optimal weight: 0.8980 chunk 37 optimal weight: 0.0030 chunk 64 optimal weight: 1.9990 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.057035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.045294 restraints weight = 59312.529| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.54 r_work: 0.2692 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7767 Z= 0.081 Angle : 0.437 12.225 10539 Z= 0.240 Chirality : 0.038 0.138 1150 Planarity : 0.003 0.040 1354 Dihedral : 6.728 148.808 1049 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.97 % Allowed : 10.63 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.28), residues: 934 helix: 1.47 (0.28), residues: 402 sheet: -0.16 (0.45), residues: 116 loop : -1.51 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 365 TYR 0.008 0.001 TYR A 515 PHE 0.010 0.001 PHE A 753 TRP 0.011 0.001 TRP A 916 HIS 0.002 0.000 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00171 / 0.08 ( 7758) covalent geometry : angle 0.43669 / 0.24 (10533) hydrogen bonds : bond 0.03509 / 2.29 ( 329) hydrogen bonds : angle 3.62871 / 2.60 ( 891) metal coordination : bond 0.00393 / 0.20 ( 8) metal coordination : angle 0.81347 / 0.34 ( 6) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 849 is missing expected H atoms. Skipping. Evaluate side-chains 46 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 44 average time/residue: 0.9657 time to fit residues: 46.0706 Evaluate side-chains 40 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 760 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 90 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 0.0770 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 909 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.054513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.042692 restraints weight = 60104.662| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.55 r_work: 0.2621 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7767 Z= 0.173 Angle : 0.495 11.937 10539 Z= 0.276 Chirality : 0.041 0.133 1150 Planarity : 0.003 0.040 1354 Dihedral : 6.899 150.631 1049 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.21 % Allowed : 10.75 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.28), residues: 934 helix: 1.39 (0.28), residues: 400 sheet: -0.26 (0.45), residues: 116 loop : -1.58 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 365 TYR 0.013 0.001 TYR A 80 PHE 0.012 0.001 PHE A 741 TRP 0.010 0.001 TRP A 916 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 ( 7758) covalent geometry : angle 0.49357 / 0.28 (10533) hydrogen bonds : bond 0.05325 / 3.44 ( 329) hydrogen bonds : angle 3.83637 / 2.73 ( 891) metal coordination : bond 0.00867 / 0.44 ( 8) metal coordination : angle 1.45687 / 0.73 ( 6) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 849 is missing expected H atoms. Skipping. Evaluate side-chains 45 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.413 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 44 average time/residue: 0.9650 time to fit residues: 46.0452 Evaluate side-chains 38 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 760 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.054061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.042352 restraints weight = 59487.566| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 2.51 r_work: 0.2608 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7767 Z= 0.178 Angle : 0.499 11.836 10539 Z= 0.278 Chirality : 0.041 0.133 1150 Planarity : 0.004 0.048 1354 Dihedral : 6.753 150.238 1047 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.21 % Allowed : 11.11 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.28), residues: 934 helix: 1.41 (0.28), residues: 395 sheet: -0.29 (0.45), residues: 116 loop : -1.53 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 365 TYR 0.013 0.001 TYR A 80 PHE 0.013 0.001 PHE A 753 TRP 0.010 0.001 TRP A 916 HIS 0.002 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 7758) covalent geometry : angle 0.49823 / 0.28 (10533) hydrogen bonds : bond 0.05455 / 3.53 ( 329) hydrogen bonds : angle 3.90138 / 2.76 ( 891) metal coordination : bond 0.00851 / 0.43 ( 8) metal coordination : angle 1.54443 / 0.76 ( 6) Misc. bond : bond 0.00044 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 849 is missing expected H atoms. Skipping. Evaluate side-chains 43 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.347 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 42 average time/residue: 0.8524 time to fit residues: 39.2934 Evaluate side-chains 39 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 760 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.054854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.043137 restraints weight = 59808.033| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 2.52 r_work: 0.2631 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7767 Z= 0.132 Angle : 0.473 11.994 10539 Z= 0.263 Chirality : 0.040 0.135 1150 Planarity : 0.003 0.039 1354 Dihedral : 6.655 149.554 1047 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.72 % Allowed : 11.71 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.28), residues: 934 helix: 1.51 (0.28), residues: 395 sheet: -0.19 (0.45), residues: 116 loop : -1.45 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 365 TYR 0.012 0.001 TYR A 80 PHE 0.012 0.001 PHE A 753 TRP 0.011 0.001 TRP A 916 HIS 0.002 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 7758) covalent geometry : angle 0.47230 / 0.26 (10533) hydrogen bonds : bond 0.04749 / 3.08 ( 329) hydrogen bonds : angle 3.81896 / 2.71 ( 891) metal coordination : bond 0.00709 / 0.35 ( 8) metal coordination : angle 1.20911 / 0.56 ( 6) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 849 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.377 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 41 average time/residue: 1.0354 time to fit residues: 45.8426 Evaluate side-chains 39 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 760 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 33 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.055287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.043548 restraints weight = 59818.512| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 2.53 r_work: 0.2641 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7767 Z= 0.121 Angle : 0.480 12.001 10539 Z= 0.263 Chirality : 0.039 0.135 1150 Planarity : 0.004 0.096 1354 Dihedral : 6.615 149.072 1047 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.85 % Allowed : 11.71 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.28), residues: 934 helix: 1.54 (0.28), residues: 397 sheet: 0.03 (0.46), residues: 111 loop : -1.41 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 18 TYR 0.011 0.001 TYR A 80 PHE 0.011 0.001 PHE A 753 TRP 0.011 0.001 TRP A 916 HIS 0.002 0.000 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 7758) covalent geometry : angle 0.47941 / 0.26 (10533) hydrogen bonds : bond 0.04495 / 2.92 ( 329) hydrogen bonds : angle 3.76280 / 2.67 ( 891) metal coordination : bond 0.00586 / 0.29 ( 8) metal coordination : angle 1.09659 / 0.49 ( 6) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 849 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.408 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 41 average time/residue: 1.0017 time to fit residues: 44.5196 Evaluate side-chains 39 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 760 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 36 optimal weight: 0.0670 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.055956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.044200 restraints weight = 59522.071| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.54 r_work: 0.2664 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7767 Z= 0.099 Angle : 0.452 12.047 10539 Z= 0.249 Chirality : 0.039 0.136 1150 Planarity : 0.004 0.088 1354 Dihedral : 6.493 147.928 1047 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.60 % Allowed : 11.96 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.28), residues: 934 helix: 1.62 (0.28), residues: 398 sheet: 0.10 (0.46), residues: 111 loop : -1.34 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 18 TYR 0.010 0.001 TYR A 80 PHE 0.010 0.001 PHE A 753 TRP 0.011 0.001 TRP A 916 HIS 0.002 0.000 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 7758) covalent geometry : angle 0.45165 / 0.25 (10533) hydrogen bonds : bond 0.04022 / 2.62 ( 329) hydrogen bonds : angle 3.68038 / 2.63 ( 891) metal coordination : bond 0.00475 / 0.24 ( 8) metal coordination : angle 0.98111 / 0.41 ( 6) Misc. bond : bond 0.00027 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 849 is missing expected H atoms. Skipping. Evaluate side-chains 39 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.406 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 38 average time/residue: 0.9474 time to fit residues: 39.3077 Evaluate side-chains 39 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 760 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.054530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.042479 restraints weight = 59267.045| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 2.60 r_work: 0.2600 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7767 Z= 0.145 Angle : 0.481 11.951 10539 Z= 0.267 Chirality : 0.040 0.133 1150 Planarity : 0.004 0.089 1354 Dihedral : 6.605 148.967 1047 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.72 % Allowed : 11.71 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.28), residues: 934 helix: 1.58 (0.28), residues: 396 sheet: 0.04 (0.46), residues: 111 loop : -1.40 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 18 TYR 0.012 0.001 TYR A 80 PHE 0.013 0.001 PHE A 753 TRP 0.010 0.001 TRP A 916 HIS 0.002 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 7758) covalent geometry : angle 0.48026 / 0.27 (10533) hydrogen bonds : bond 0.04908 / 3.18 ( 329) hydrogen bonds : angle 3.79234 / 2.69 ( 891) metal coordination : bond 0.00720 / 0.36 ( 8) metal coordination : angle 1.36789 / 0.63 ( 6) Misc. bond : bond 0.00040 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4284.30 seconds wall clock time: 73 minutes 18.79 seconds (4398.79 seconds total)