Starting phenix.real_space_refine on Thu Aug 6 21:01:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byp_45041/08_2026/9byp_45041.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byp_45041/08_2026/9byp_45041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9byp_45041/08_2026/9byp_45041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byp_45041/08_2026/9byp_45041.map" model { file = "/net/cci-nas-00/data/ceres_data/9byp_45041/08_2026/9byp_45041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byp_45041/08_2026/9byp_45041.cif" } resolution = 2.2 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= 0.016 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 1 6.06 5 P 11 5.49 5 S 47 5.16 5 C 5258 2.51 5 N 1438 2.21 5 O 1873 1.98 5 H 8681 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 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: 17309 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 14617 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 948, 14593 Classifications: {'peptide': 948} Link IDs: {'PTRANS': 63, 'TRANS': 884} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 948, 14593 Classifications: {'peptide': 948} Link IDs: {'PTRANS': 63, 'TRANS': 884} Chain breaks: 2 bond proxies already assigned to first conformer: 14750 Chain: "C" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 376 Classifications: {'DNA': 12} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 11} Chain: "B" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1472 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain breaks: 1 Chain: "A" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 817 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1, 'water': 272} Link IDs: {None: 272} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 21 Classifications: {'water': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6687 SG CYS A 453 41.438 65.878 81.381 1.00 57.64 S ATOM 6727 SG CYS A 456 44.522 67.319 80.372 1.00 53.48 S ATOM 6833 SG CYS A 464 43.501 64.530 78.586 1.00 59.44 S Time building chain proxies: 3.85, per 1000 atoms: 0.22 Number of scatterers: 17309 At special positions: 0 Unit cell: (89.04, 91.56, 112.56, 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 1 29.99 S 47 16.00 P 11 15.00 O 1873 8.00 N 1438 7.00 C 5258 6.00 H 8681 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: 1.36 Conformation dependent library (CDL) restraints added in 681.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 456 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 464 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 453 " 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 7 sheets defined 51.3% alpha, 19.4% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 32 through 40 removed outlier: 3.560A pdb=" N THR A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 107 through 119 removed outlier: 3.727A pdb=" N GLU A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 157 through 163 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.732A pdb=" N LEU A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 266 through 291 Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 296 through 308 removed outlier: 4.791A pdb=" N TYR A 301 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASP A 302 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 305 - end of helix Processing helix chain 'A' and resid 311 through 337 removed outlier: 4.399A pdb=" N ALA A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 357 through 360 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.669A pdb=" N GLU A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 410 removed outlier: 3.624A pdb=" N LEU A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 425 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 464 through 473 Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 526 through 540 Processing helix chain 'A' and resid 555 through 584 removed outlier: 3.549A pdb=" N PHE A 563 " --> pdb=" O PHE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.539A pdb=" N LEU A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 608 removed outlier: 3.741A pdb=" N GLN A 608 " --> pdb=" O PRO A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 641 removed outlier: 3.728A pdb=" N THR A 615 " --> pdb=" O CYS A 611 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN A 616 " --> pdb=" O PRO A 612 " (cutoff:3.500A) Proline residue: A 632 - end of helix Processing helix chain 'A' and resid 647 through 667 removed outlier: 4.093A pdb=" N GLY A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN A 657 " --> pdb=" O LYS A 653 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N THR A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 697 removed outlier: 3.874A pdb=" N GLN A 697 " --> pdb=" O ASP A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 739 Processing helix chain 'A' and resid 746 through 750 removed outlier: 3.862A pdb=" N TYR A 749 " --> pdb=" O ARG A 746 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE A 750 " --> pdb=" O GLU A 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 746 through 750' Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 762 through 767 Processing helix chain 'A' and resid 773 through 785 Processing helix chain 'A' and resid 794 through 816 Processing helix chain 'A' and resid 824 through 841 Processing helix chain 'A' and resid 864 through 871 Proline residue: A 867 - end of helix Processing helix chain 'A' and resid 877 through 886 Processing helix chain 'A' and resid 900 through 907 removed outlier: 3.933A pdb=" N VAL A 904 " --> pdb=" O CYS A 900 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 907 " --> pdb=" O GLN A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 948 Processing helix chain 'B' and resid 989 through 1004 removed outlier: 3.500A pdb=" N ASN B 993 " --> pdb=" O TYR B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1023 Processing helix chain 'B' and resid 1024 through 1029 Processing helix chain 'B' and resid 1030 through 1038 Processing helix chain 'B' and resid 1039 through 1043 removed outlier: 3.590A pdb=" N SER B1042 " --> pdb=" O GLY B1039 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL B1043 " --> pdb=" O ARG B1040 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1039 through 1043' Processing helix chain 'B' and resid 1044 through 1057 Processing helix chain 'B' and resid 1063 through 1075 removed outlier: 3.954A pdb=" N TRP B1075 " --> pdb=" O LEU B1071 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 removed outlier: 7.113A pdb=" N GLY A 18 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N ARG A 72 " --> pdb=" O GLY A 18 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU A 80 " --> pdb=" O HIS A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 52 removed outlier: 6.891A pdb=" N ASP A 89 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ILE A 153 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY A 149 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA A 182 " --> pdb=" O PRO A 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 52 removed outlier: 6.891A pdb=" N ASP A 89 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ILE A 153 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY A 149 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA A 182 " --> pdb=" O PRO A 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 344 through 349 removed outlier: 3.683A pdb=" N GLY A 346 " --> pdb=" O THR A 365 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 493 removed outlier: 22.849A pdb=" N ILE A 929 " --> pdb=" O PRO A 717 " (cutoff:3.500A) removed outlier: 17.190A pdb=" N ASN A 719 " --> pdb=" O ILE A 929 " (cutoff:3.500A) removed outlier: 12.361A pdb=" N GLN A 931 " --> pdb=" O ASN A 719 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N LYS A 721 " --> pdb=" O GLN A 931 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY A 933 " --> pdb=" O LYS A 721 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ARG A 725 " --> pdb=" O LEU A 935 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR A 674 " --> pdb=" O ARG A 718 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 596 through 602 removed outlier: 22.849A pdb=" N ILE A 929 " --> pdb=" O PRO A 717 " (cutoff:3.500A) removed outlier: 17.190A pdb=" N ASN A 719 " --> pdb=" O ILE A 929 " (cutoff:3.500A) removed outlier: 12.361A pdb=" N GLN A 931 " --> pdb=" O ASN A 719 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N LYS A 721 " --> pdb=" O GLN A 931 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY A 933 " --> pdb=" O LYS A 721 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ARG A 725 " --> pdb=" O LEU A 935 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N PHE A 968 " --> pdb=" O PRO A 914 " (cutoff:3.500A) removed outlier: 14.096A pdb=" N THR A 916 " --> pdb=" O LYS A 966 " (cutoff:3.500A) removed outlier: 16.743A pdb=" N LYS A 966 " --> pdb=" O THR A 916 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 853 " --> pdb=" O THR A 898 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 786 through 788 416 hydrogen bonds defined for protein. 1140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.09: 2911 1.09 - 1.27: 7093 1.27 - 1.46: 2525 1.46 - 1.64: 4652 1.64 - 1.83: 65 Bond restraints: 17246 Sorted by residual: bond pdb=" N CYS A 900 " pdb=" H CYS A 900 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" N ARG B1068 " pdb=" H ARG B1068 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" NH2 ARG A 857 " pdb="HH22 ARG A 857 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N GLY A 389 " pdb=" H GLY A 389 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N LEU A 705 " pdb=" H LEU A 705 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 ... (remaining 17241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 25403 2.68 - 5.36: 3969 5.36 - 8.03: 967 8.03 - 10.71: 22 10.71 - 13.39: 24 Bond angle restraints: 30385 Sorted by residual: angle pdb=" O5' DC C 12 " pdb=" C5' DC C 12 " pdb=" C4' DC C 12 " ideal model delta sigma weight residual 109.40 118.66 -9.26 8.00e-01 1.56e+00 1.34e+02 angle pdb=" N6 DA C 3 " pdb=" C6 DA C 3 " pdb=" N1 DA C 3 " ideal model delta sigma weight residual 118.60 112.87 5.73 6.00e-01 2.78e+00 9.13e+01 angle pdb=" N6 DA C 6 " pdb=" C6 DA C 6 " pdb=" N1 DA C 6 " ideal model delta sigma weight residual 118.60 113.08 5.52 6.00e-01 2.78e+00 8.45e+01 angle pdb=" N6 DA C 5 " pdb=" C6 DA C 5 " pdb=" N1 DA C 5 " ideal model delta sigma weight residual 118.60 113.20 5.40 6.00e-01 2.78e+00 8.09e+01 angle pdb=" O5' DC C 2 " pdb=" C5' DC C 2 " pdb=" C4' DC C 2 " ideal model delta sigma weight residual 109.40 116.41 -7.01 8.00e-01 1.56e+00 7.67e+01 ... (remaining 30380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 7197 17.61 - 35.22: 422 35.22 - 52.83: 173 52.83 - 70.44: 122 70.44 - 88.05: 7 Dihedral angle restraints: 7921 sinusoidal: 4344 harmonic: 3577 Sorted by residual: dihedral pdb=" CA SER B1058 " pdb=" C SER B1058 " pdb=" N GLY B1059 " pdb=" CA GLY B1059 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA SER A 962 " pdb=" C SER A 962 " pdb=" N SER A 963 " pdb=" CA SER A 963 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA PRO A 909 " pdb=" C PRO A 909 " pdb=" N VAL A 910 " pdb=" CA VAL A 910 " ideal model delta harmonic sigma weight residual 180.00 156.83 23.17 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 7918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 686 0.075 - 0.149: 418 0.149 - 0.224: 152 0.224 - 0.298: 37 0.298 - 0.373: 7 Chirality restraints: 1300 Sorted by residual: chirality pdb=" CA PRO A 648 " pdb=" N PRO A 648 " pdb=" C PRO A 648 " pdb=" CB PRO A 648 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA ARG A 965 " pdb=" N ARG A 965 " pdb=" C ARG A 965 " pdb=" CB ARG A 965 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA ASP A 302 " pdb=" N ASP A 302 " pdb=" C ASP A 302 " pdb=" CB ASP A 302 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 1297 not shown) Planarity restraints: 2476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 228 " -0.483 9.50e-02 1.11e+02 1.91e-01 2.64e+02 pdb=" NE ARG A 228 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 228 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 228 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG A 228 " 0.014 2.00e-02 2.50e+03 pdb="HH11 ARG A 228 " 0.172 2.00e-02 2.50e+03 pdb="HH12 ARG A 228 " -0.199 2.00e-02 2.50e+03 pdb="HH21 ARG A 228 " -0.056 2.00e-02 2.50e+03 pdb="HH22 ARG A 228 " 0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1031 " 0.387 9.50e-02 1.11e+02 1.61e-01 2.26e+02 pdb=" NE ARG B1031 " 0.075 2.00e-02 2.50e+03 pdb=" CZ ARG B1031 " 0.052 2.00e-02 2.50e+03 pdb=" NH1 ARG B1031 " 0.098 2.00e-02 2.50e+03 pdb=" NH2 ARG B1031 " -0.010 2.00e-02 2.50e+03 pdb="HH11 ARG B1031 " -0.222 2.00e-02 2.50e+03 pdb="HH12 ARG B1031 " 0.094 2.00e-02 2.50e+03 pdb="HH21 ARG B1031 " -0.085 2.00e-02 2.50e+03 pdb="HH22 ARG B1031 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 810 " 0.072 9.50e-02 1.11e+02 8.96e-02 1.68e+02 pdb=" NE ARG A 810 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 810 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 810 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 810 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 810 " -0.118 2.00e-02 2.50e+03 pdb="HH12 ARG A 810 " 0.173 2.00e-02 2.50e+03 pdb="HH21 ARG A 810 " 0.055 2.00e-02 2.50e+03 pdb="HH22 ARG A 810 " -0.138 2.00e-02 2.50e+03 ... (remaining 2473 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1339 2.18 - 2.78: 28469 2.78 - 3.39: 49601 3.39 - 3.99: 69764 3.99 - 4.60: 98426 Nonbonded interactions: 247599 Sorted by model distance: nonbonded pdb="HD21AASN A 300 " pdb=" OG SER A 303 " model vdw 1.571 2.450 nonbonded pdb=" OE2 GLU A 797 " pdb=" H1 HOH A2101 " model vdw 1.582 2.450 nonbonded pdb="HH22 ARG A 88 " pdb=" O PRO A 609 " model vdw 1.596 2.450 nonbonded pdb=" HH TYR A 24 " pdb=" OE1 GLU A 60 " model vdw 1.602 2.450 nonbonded pdb=" HG SER A 350 " pdb=" OE1 GLU A 356 " model vdw 1.617 2.450 ... (remaining 247594 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=0.12 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: 2.120 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: 0.100 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 19.980 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:4.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 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 : 0.013 0.289 8568 Z= 0.865 Angle : 1.902 9.259 11692 Z= 1.382 Chirality : 0.105 0.373 1300 Planarity : 0.017 0.186 1487 Dihedral : 13.286 88.045 3156 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 0.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.11 % Allowed : 1.48 % Favored : 98.40 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.23), residues: 1037 helix: -0.71 (0.21), residues: 457 sheet: 0.55 (0.52), residues: 89 loop : -0.23 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG A 810 TYR 0.120 0.025 TYR A 866 PHE 0.068 0.013 PHE A 157 TRP 0.122 0.020 TRP A 778 HIS 0.015 0.003 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.01292 / 0.86 ( 8565) covalent geometry : angle 1.90232 / 1.38 (11692) hydrogen bonds : bond 0.22629 / 14.98 ( 389) hydrogen bonds : angle 6.83536 / 4.83 ( 1140) metal coordination : bond 0.20539 / 9.96 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 TYR cc_start: 0.8518 (m-80) cc_final: 0.8230 (m-80) REVERT: A 714 MET cc_start: 0.9211 (ttm) cc_final: 0.8845 (ttp) REVERT: A 756 MET cc_start: 0.9352 (tpt) cc_final: 0.8692 (tpt) REVERT: A 939 MET cc_start: 0.9538 (mtp) cc_final: 0.9080 (mtp) REVERT: B 1032 ASP cc_start: 0.8679 (m-30) cc_final: 0.8459 (m-30) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 1.2483 time to fit residues: 192.0781 Evaluate side-chains 96 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 430 GLN A 639 ASN A 736 GLN A 779 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.090854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.068013 restraints weight = 39732.456| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.07 r_work: 0.2695 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 8568 Z= 0.195 Angle : 0.748 8.208 11692 Z= 0.420 Chirality : 0.048 0.155 1300 Planarity : 0.008 0.093 1487 Dihedral : 10.900 85.934 1275 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.57 % Allowed : 6.50 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.25), residues: 1037 helix: 0.43 (0.24), residues: 469 sheet: 0.21 (0.41), residues: 118 loop : -0.28 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 703 TYR 0.028 0.002 TYR A 798 PHE 0.016 0.002 PHE A 412 TRP 0.012 0.002 TRP B1075 HIS 0.009 0.002 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.20 ( 8565) covalent geometry : angle 0.74760 / 0.42 (11692) hydrogen bonds : bond 0.08034 / 5.22 ( 389) hydrogen bonds : angle 5.28471 / 3.74 ( 1140) metal coordination : bond 0.00653 / 0.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8156 (mp0) REVERT: A 546 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8035 (mm-30) REVERT: A 688 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.7926 (m-30) REVERT: A 714 MET cc_start: 0.9154 (ttm) cc_final: 0.8848 (ttp) REVERT: A 747 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8141 (mm-30) REVERT: A 756 MET cc_start: 0.9323 (tpt) cc_final: 0.8357 (tpt) REVERT: A 903 GLN cc_start: 0.8280 (mm-40) cc_final: 0.7902 (tp-100) REVERT: A 939 MET cc_start: 0.9504 (mtp) cc_final: 0.9119 (mtp) REVERT: B 1084 ASN cc_start: 0.7585 (p0) cc_final: 0.7316 (p0) outliers start: 5 outliers final: 2 residues processed: 101 average time/residue: 1.3786 time to fit residues: 147.2646 Evaluate side-chains 94 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 765 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 54 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 72 optimal weight: 0.0470 chunk 68 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.0470 chunk 81 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN A A 584 ASN A 924 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.091405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.068388 restraints weight = 43572.846| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.15 r_work: 0.2703 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8568 Z= 0.140 Angle : 0.598 4.755 11692 Z= 0.331 Chirality : 0.043 0.150 1300 Planarity : 0.005 0.057 1487 Dihedral : 10.547 82.919 1275 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.80 % Allowed : 6.84 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.25), residues: 1037 helix: 1.07 (0.25), residues: 467 sheet: 0.15 (0.41), residues: 118 loop : -0.32 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 703 TYR 0.019 0.002 TYR A 527 PHE 0.013 0.002 PHE A 506 TRP 0.010 0.001 TRP A 778 HIS 0.015 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 8565) covalent geometry : angle 0.59811 / 0.33 (11692) hydrogen bonds : bond 0.05957 / 3.93 ( 389) hydrogen bonds : angle 4.78519 / 3.37 ( 1140) metal coordination : bond 0.00433 / 0.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: A 688 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8140 (m-30) REVERT: A 714 MET cc_start: 0.9089 (ttm) cc_final: 0.8834 (ttp) REVERT: A 747 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8235 (mm-30) REVERT: A 756 MET cc_start: 0.9349 (tpt) cc_final: 0.8657 (tpt) REVERT: A 864 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8695 (ttp-110) REVERT: A 939 MET cc_start: 0.9465 (mtp) cc_final: 0.9120 (mtp) outliers start: 7 outliers final: 2 residues processed: 99 average time/residue: 1.3665 time to fit residues: 142.4075 Evaluate side-chains 95 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 864 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 59 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 3 optimal weight: 0.0670 chunk 1 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 655 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.091480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.068768 restraints weight = 39965.511| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.07 r_work: 0.2713 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8568 Z= 0.129 Angle : 0.556 5.232 11692 Z= 0.306 Chirality : 0.042 0.142 1300 Planarity : 0.005 0.087 1487 Dihedral : 10.502 80.162 1275 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.80 % Allowed : 7.87 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.26), residues: 1037 helix: 1.27 (0.25), residues: 467 sheet: 0.08 (0.41), residues: 118 loop : -0.28 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 746 TYR 0.018 0.002 TYR A 798 PHE 0.012 0.001 PHE A 506 TRP 0.010 0.001 TRP A 778 HIS 0.009 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 8565) covalent geometry : angle 0.55647 / 0.31 (11692) hydrogen bonds : bond 0.05471 / 3.62 ( 389) hydrogen bonds : angle 4.61647 / 3.24 ( 1140) metal coordination : bond 0.00376 / 0.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 714 MET cc_start: 0.9090 (ttm) cc_final: 0.8823 (ttp) REVERT: A 746 ARG cc_start: 0.8277 (mmt90) cc_final: 0.7936 (tpp80) REVERT: A 747 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8267 (mm-30) REVERT: A 756 MET cc_start: 0.9321 (tpt) cc_final: 0.8679 (tpt) REVERT: A 864 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8473 (ttp-110) REVERT: A 939 MET cc_start: 0.9445 (mtp) cc_final: 0.9094 (mtp) outliers start: 7 outliers final: 1 residues processed: 96 average time/residue: 1.5525 time to fit residues: 156.7043 Evaluate side-chains 93 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 864 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 60 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3165 r_free = 0.3165 target = 0.088642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.065897 restraints weight = 39229.334| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.05 r_work: 0.2659 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8568 Z= 0.218 Angle : 0.612 5.335 11692 Z= 0.338 Chirality : 0.045 0.170 1300 Planarity : 0.006 0.093 1487 Dihedral : 10.472 79.371 1275 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.80 % Allowed : 7.98 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.45 (0.26), residues: 1037 helix: 1.14 (0.25), residues: 467 sheet: -0.15 (0.39), residues: 131 loop : -0.38 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 746 TYR 0.025 0.002 TYR A 798 PHE 0.016 0.002 PHE A 412 TRP 0.010 0.001 TRP A 778 HIS 0.011 0.002 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.22 ( 8565) covalent geometry : angle 0.61169 / 0.34 (11692) hydrogen bonds : bond 0.06609 / 4.42 ( 389) hydrogen bonds : angle 4.68335 / 3.29 ( 1140) metal coordination : bond 0.00708 / 0.36 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: A 714 MET cc_start: 0.9184 (ttm) cc_final: 0.8840 (ttp) REVERT: A 746 ARG cc_start: 0.8377 (mmt90) cc_final: 0.8069 (mmt90) REVERT: A 747 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8270 (mm-30) REVERT: A 756 MET cc_start: 0.9319 (tpt) cc_final: 0.8774 (tpt) REVERT: A 864 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8748 (ttp-110) REVERT: A 939 MET cc_start: 0.9432 (mtp) cc_final: 0.9139 (mtp) outliers start: 7 outliers final: 3 residues processed: 97 average time/residue: 1.5126 time to fit residues: 154.5311 Evaluate side-chains 97 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 864 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 92 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 554 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.090303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.067592 restraints weight = 42313.009| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.10 r_work: 0.2694 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8568 Z= 0.126 Angle : 0.545 5.402 11692 Z= 0.298 Chirality : 0.041 0.144 1300 Planarity : 0.006 0.084 1487 Dihedral : 10.435 77.770 1275 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.57 % Allowed : 8.44 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.26), residues: 1037 helix: 1.34 (0.25), residues: 467 sheet: -0.04 (0.40), residues: 128 loop : -0.38 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 704 TYR 0.017 0.002 TYR A 798 PHE 0.012 0.001 PHE A 506 TRP 0.011 0.001 TRP A 778 HIS 0.009 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 8565) covalent geometry : angle 0.54537 / 0.30 (11692) hydrogen bonds : bond 0.05272 / 3.50 ( 389) hydrogen bonds : angle 4.44594 / 3.07 ( 1140) metal coordination : bond 0.00386 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: A 714 MET cc_start: 0.9158 (ttm) cc_final: 0.8868 (ttp) REVERT: A 746 ARG cc_start: 0.8340 (mmt90) cc_final: 0.8035 (mmt90) REVERT: A 747 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8304 (mm-30) REVERT: A 756 MET cc_start: 0.9293 (tpt) cc_final: 0.8784 (tpt) REVERT: A 864 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8356 (ttp-110) REVERT: A 939 MET cc_start: 0.9423 (mtp) cc_final: 0.9134 (mtp) outliers start: 5 outliers final: 1 residues processed: 94 average time/residue: 1.4490 time to fit residues: 143.0603 Evaluate side-chains 93 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 864 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 554 HIS B1004 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.089492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.066928 restraints weight = 39411.159| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.05 r_work: 0.2684 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9141 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8568 Z= 0.169 Angle : 0.567 5.687 11692 Z= 0.310 Chirality : 0.043 0.158 1300 Planarity : 0.006 0.092 1487 Dihedral : 10.402 77.386 1275 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.46 % Allowed : 8.55 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.26), residues: 1037 helix: 1.34 (0.25), residues: 467 sheet: -0.18 (0.39), residues: 132 loop : -0.40 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 704 TYR 0.021 0.002 TYR A 798 PHE 0.012 0.002 PHE A 412 TRP 0.010 0.001 TRP A 778 HIS 0.008 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 ( 8565) covalent geometry : angle 0.56657 / 0.31 (11692) hydrogen bonds : bond 0.05762 / 3.86 ( 389) hydrogen bonds : angle 4.46804 / 3.09 ( 1140) metal coordination : bond 0.00490 / 0.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: A 314 GLU cc_start: 0.8059 (mp0) cc_final: 0.7854 (mp0) REVERT: A 714 MET cc_start: 0.9176 (ttm) cc_final: 0.8897 (ttp) REVERT: A 746 ARG cc_start: 0.8385 (mmt90) cc_final: 0.8076 (mmt90) REVERT: A 747 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8279 (mm-30) REVERT: A 756 MET cc_start: 0.9298 (tpt) cc_final: 0.8742 (tpt) REVERT: A 769 ASP cc_start: 0.8368 (p0) cc_final: 0.8104 (p0) REVERT: A 939 MET cc_start: 0.9407 (mtp) cc_final: 0.9122 (mtp) outliers start: 4 outliers final: 2 residues processed: 96 average time/residue: 1.4131 time to fit residues: 142.8106 Evaluate side-chains 92 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 744 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 554 HIS B1004 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.091011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.068292 restraints weight = 39661.743| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.07 r_work: 0.2707 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8568 Z= 0.117 Angle : 0.534 6.188 11692 Z= 0.290 Chirality : 0.041 0.144 1300 Planarity : 0.006 0.093 1487 Dihedral : 10.385 77.268 1275 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.46 % Allowed : 8.78 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.26), residues: 1037 helix: 1.47 (0.25), residues: 468 sheet: -0.16 (0.40), residues: 130 loop : -0.36 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 704 TYR 0.015 0.001 TYR A 798 PHE 0.012 0.001 PHE A 506 TRP 0.011 0.001 TRP A 778 HIS 0.007 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 8565) covalent geometry : angle 0.53374 / 0.29 (11692) hydrogen bonds : bond 0.04990 / 3.32 ( 389) hydrogen bonds : angle 4.37251 / 3.00 ( 1140) metal coordination : bond 0.00291 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: A 314 GLU cc_start: 0.7984 (mp0) cc_final: 0.7748 (mp0) REVERT: A 714 MET cc_start: 0.9162 (ttm) cc_final: 0.8881 (ttp) REVERT: A 746 ARG cc_start: 0.8352 (mmt90) cc_final: 0.8042 (mmt90) REVERT: A 747 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8284 (mm-30) REVERT: A 756 MET cc_start: 0.9284 (tpt) cc_final: 0.8773 (tpt) REVERT: A 769 ASP cc_start: 0.8353 (p0) cc_final: 0.8096 (p0) REVERT: A 939 MET cc_start: 0.9393 (mtp) cc_final: 0.9110 (mtp) outliers start: 4 outliers final: 1 residues processed: 93 average time/residue: 1.4942 time to fit residues: 146.4208 Evaluate side-chains 89 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 738 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 554 HIS B1004 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.091018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.067700 restraints weight = 46743.751| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.22 r_work: 0.2694 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8568 Z= 0.130 Angle : 0.535 6.681 11692 Z= 0.289 Chirality : 0.041 0.145 1300 Planarity : 0.005 0.096 1487 Dihedral : 10.335 76.775 1275 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.23 % Allowed : 9.24 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.78 (0.26), residues: 1037 helix: 1.54 (0.25), residues: 468 sheet: -0.08 (0.42), residues: 120 loop : -0.34 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 704 TYR 0.017 0.002 TYR A 798 PHE 0.012 0.001 PHE A 506 TRP 0.011 0.001 TRP A 778 HIS 0.007 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 8565) covalent geometry : angle 0.53481 / 0.29 (11692) hydrogen bonds : bond 0.04933 / 3.30 ( 389) hydrogen bonds : angle 4.33783 / 2.97 ( 1140) metal coordination : bond 0.00335 / 0.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: A 714 MET cc_start: 0.9140 (ttm) cc_final: 0.8877 (ttp) REVERT: A 746 ARG cc_start: 0.8390 (mmt90) cc_final: 0.8080 (mmt90) REVERT: A 747 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8305 (mm-30) REVERT: A 756 MET cc_start: 0.9286 (tpt) cc_final: 0.8757 (tpt) REVERT: A 769 ASP cc_start: 0.8358 (p0) cc_final: 0.8099 (p0) REVERT: A 939 MET cc_start: 0.9391 (mtp) cc_final: 0.9116 (mtp) outliers start: 2 outliers final: 1 residues processed: 90 average time/residue: 1.3460 time to fit residues: 127.5507 Evaluate side-chains 89 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 738 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 56 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 554 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.090971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.068071 restraints weight = 41491.047| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.10 r_work: 0.2702 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8568 Z= 0.131 Angle : 0.533 6.484 11692 Z= 0.289 Chirality : 0.041 0.148 1300 Planarity : 0.005 0.095 1487 Dihedral : 10.329 76.243 1275 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.34 % Allowed : 9.35 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.26), residues: 1037 helix: 1.55 (0.25), residues: 469 sheet: -0.07 (0.42), residues: 120 loop : -0.37 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 704 TYR 0.017 0.002 TYR A 798 PHE 0.011 0.001 PHE A 506 TRP 0.011 0.001 TRP A 778 HIS 0.007 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 8565) covalent geometry : angle 0.53278 / 0.29 (11692) hydrogen bonds : bond 0.04965 / 3.32 ( 389) hydrogen bonds : angle 4.32855 / 2.97 ( 1140) metal coordination : bond 0.00334 / 0.17 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: A 314 GLU cc_start: 0.7941 (mp0) cc_final: 0.7711 (mp0) REVERT: A 714 MET cc_start: 0.9142 (ttm) cc_final: 0.8876 (ttp) REVERT: A 746 ARG cc_start: 0.8384 (mmt90) cc_final: 0.8073 (mmt90) REVERT: A 747 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8297 (mm-30) REVERT: A 756 MET cc_start: 0.9282 (tpt) cc_final: 0.8771 (tpt) REVERT: A 769 ASP cc_start: 0.8338 (p0) cc_final: 0.8057 (p0) REVERT: A 939 MET cc_start: 0.9383 (mtp) cc_final: 0.9104 (mtp) outliers start: 3 outliers final: 2 residues processed: 89 average time/residue: 1.4218 time to fit residues: 133.3848 Evaluate side-chains 90 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 744 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 53 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 76 optimal weight: 0.0980 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 554 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.092228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.069579 restraints weight = 40416.787| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.08 r_work: 0.2733 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9106 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8568 Z= 0.106 Angle : 0.515 6.812 11692 Z= 0.277 Chirality : 0.040 0.140 1300 Planarity : 0.005 0.098 1487 Dihedral : 10.294 75.889 1275 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.23 % Allowed : 9.58 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.26), residues: 1037 helix: 1.70 (0.25), residues: 469 sheet: -0.03 (0.42), residues: 120 loop : -0.31 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 704 TYR 0.013 0.001 TYR A 527 PHE 0.011 0.001 PHE A 506 TRP 0.011 0.001 TRP A 778 HIS 0.007 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 8565) covalent geometry : angle 0.51495 / 0.28 (11692) hydrogen bonds : bond 0.04329 / 2.89 ( 389) hydrogen bonds : angle 4.23732 / 2.89 ( 1140) metal coordination : bond 0.00150 / 0.08 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6388.88 seconds wall clock time: 108 minutes 18.70 seconds (6498.70 seconds total)