Starting phenix.real_space_refine on Wed Aug 5 19:30:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qwf_18694/08_2026/8qwf_18694.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qwf_18694/08_2026/8qwf_18694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qwf_18694/08_2026/8qwf_18694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qwf_18694/08_2026/8qwf_18694.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qwf_18694/08_2026/8qwf_18694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qwf_18694/08_2026/8qwf_18694.map" } resolution = 3.08 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 77 5.49 5 Mg 6 5.21 5 S 18 5.16 5 C 7067 2.51 5 N 1911 2.21 5 O 2422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 11501 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1186, 9895 Classifications: {'peptide': 1186} Link IDs: {'PTRANS': 30, 'TRANS': 1155} Chain breaks: 6 Chain: "C" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 697 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 11, 'rna3p_pyr': 13} Link IDs: {'rna2p': 8, 'rna3p': 24} Chain: "T" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 581 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "N" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 322 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.82, per 1000 atoms: 0.16 Number of scatterers: 11501 At special positions: 0 Unit cell: (95.5608, 99.6798, 141.694, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 77 15.00 Mg 6 11.99 O 2422 8.00 N 1911 7.00 C 7067 6.00 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: 0.63 Conformation dependent library (CDL) restraints added in 307.8 milliseconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2276 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 48.3% alpha, 11.0% beta 25 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 removed outlier: 4.404A pdb=" N ASN A 7 " --> pdb=" O LYS A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 36 Processing helix chain 'A' and resid 38 through 67 removed outlier: 3.506A pdb=" N ALA A 45 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 85 Processing helix chain 'A' and resid 92 through 117 removed outlier: 4.076A pdb=" N PHE A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 125 through 131 removed outlier: 4.167A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 161 through 170 removed outlier: 3.831A pdb=" N ASN A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 188 removed outlier: 3.523A pdb=" N ARG A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 207 removed outlier: 3.666A pdb=" N LYS A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.666A pdb=" N ILE A 234 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 244 Processing helix chain 'A' and resid 245 through 257 Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 315 through 331 removed outlier: 3.565A pdb=" N LEU A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 351 removed outlier: 3.601A pdb=" N LYS A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 376 removed outlier: 4.074A pdb=" N THR A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 389 Processing helix chain 'A' and resid 422 through 430 Processing helix chain 'A' and resid 445 through 456 Processing helix chain 'A' and resid 491 through 510 Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 527 through 542 removed outlier: 4.701A pdb=" N GLU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU A 540 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 556 removed outlier: 3.656A pdb=" N THR A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 584 removed outlier: 3.573A pdb=" N GLU A 583 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR A 584 " --> pdb=" O ASN A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 584' Processing helix chain 'A' and resid 633 through 643 Proline residue: A 639 - end of helix Processing helix chain 'A' and resid 647 through 652 Processing helix chain 'A' and resid 654 through 664 Processing helix chain 'A' and resid 674 through 692 Processing helix chain 'A' and resid 695 through 699 removed outlier: 3.640A pdb=" N GLY A 699 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 708 Processing helix chain 'A' and resid 710 through 722 removed outlier: 4.012A pdb=" N PHE A 714 " --> pdb=" O ASP A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 751 through 755 removed outlier: 3.637A pdb=" N SER A 755 " --> pdb=" O LYS A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 773 removed outlier: 4.103A pdb=" N PHE A 773 " --> pdb=" O TRP A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 780 Processing helix chain 'A' and resid 831 through 835 Processing helix chain 'A' and resid 857 through 868 Processing helix chain 'A' and resid 914 through 931 removed outlier: 3.758A pdb=" N LYS A 923 " --> pdb=" O ASP A 919 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS A 930 " --> pdb=" O ASP A 926 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER A 931 " --> pdb=" O LYS A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 961 removed outlier: 3.590A pdb=" N LEU A 946 " --> pdb=" O LYS A 942 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER A 947 " --> pdb=" O GLU A 943 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN A 948 " --> pdb=" O GLY A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 998 removed outlier: 3.888A pdb=" N TYR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1072 removed outlier: 3.755A pdb=" N LYS A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1094 No H-bonds generated for 'chain 'A' and resid 1092 through 1094' Processing helix chain 'A' and resid 1130 through 1141 Processing helix chain 'A' and resid 1161 through 1175 Processing helix chain 'A' and resid 1216 through 1237 removed outlier: 3.812A pdb=" N ALA A1220 " --> pdb=" O ASP A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1257 Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 567 removed outlier: 4.796A pdb=" N VAL A 791 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE A 839 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 22 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TYR A 597 " --> pdb=" O ILE A 749 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 564 through 567 removed outlier: 4.796A pdb=" N VAL A 791 " --> pdb=" O LEU A 567 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 363 Processing sheet with id=AA4, first strand: chain 'A' and resid 622 through 630 removed outlier: 3.622A pdb=" N ILE A 730 " --> pdb=" O TYR A 623 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 803 through 804 Processing sheet with id=AA6, first strand: chain 'A' and resid 810 through 811 Processing sheet with id=AA7, first strand: chain 'A' and resid 896 through 901 removed outlier: 6.886A pdb=" N LEU A 889 " --> pdb=" O VAL A 897 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLN A 899 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU A 887 " --> pdb=" O GLN A 899 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN A 873 " --> pdb=" O ILE A 963 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL A 965 " --> pdb=" O ASN A 873 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE A 875 " --> pdb=" O VAL A 965 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N GLU A 967 " --> pdb=" O ILE A 875 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N ILE A 877 " --> pdb=" O GLU A 967 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N PHE A1036 " --> pdb=" O ALA A 962 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL A 964 " --> pdb=" O PHE A1036 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL A1038 " --> pdb=" O VAL A 964 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N MET A 966 " --> pdb=" O VAL A1038 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 904 through 905 Processing sheet with id=AA9, first strand: chain 'A' and resid 1075 through 1079 removed outlier: 4.109A pdb=" N TYR A1084 " --> pdb=" O ASN A1079 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE A1089 " --> pdb=" O TRP A1103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1179 through 1181 removed outlier: 4.964A pdb=" N PHE A1202 " --> pdb=" O SER A1192 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1194 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 116 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2850 1.33 - 1.45: 2645 1.45 - 1.57: 6211 1.57 - 1.69: 151 1.69 - 1.81: 32 Bond restraints: 11889 Sorted by residual: bond pdb=" C3' DG N -8 " pdb=" C2' DG N -8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.81e+00 bond pdb=" C1' DT N -10 " pdb=" N1 DT N -10 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 8.93e+00 bond pdb=" C3' DC N -11 " pdb=" C2' DC N -11 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.47e+00 bond pdb=" C1' DC T -8 " pdb=" N1 DC T -8 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.67e+00 bond pdb=" C3' DC T -10 " pdb=" C2' DC T -10 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.40e+00 ... (remaining 11884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 16040 2.04 - 4.09: 275 4.09 - 6.13: 13 6.13 - 8.17: 4 8.17 - 10.22: 1 Bond angle restraints: 16333 Sorted by residual: angle pdb=" C1' C C -10 " pdb=" N1 C C -10 " pdb=" C2 C C -10 " ideal model delta sigma weight residual 118.80 123.68 -4.88 1.10e+00 8.26e-01 1.97e+01 angle pdb=" N3 DT T -13 " pdb=" C4 DT T -13 " pdb=" O4 DT T -13 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT N 1 " pdb=" C4 DT N 1 " pdb=" O4 DT N 1 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT T 0 " pdb=" C4 DT T 0 " pdb=" O4 DT T 0 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT N -10 " pdb=" C4 DT N -10 " pdb=" O4 DT N -10 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 ... (remaining 16328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.78: 6763 33.78 - 67.56: 346 67.56 - 101.34: 27 101.34 - 135.11: 0 135.11 - 168.89: 1 Dihedral angle restraints: 7137 sinusoidal: 3620 harmonic: 3517 Sorted by residual: dihedral pdb=" CA HIS A 207 " pdb=" C HIS A 207 " pdb=" N PRO A 208 " pdb=" CA PRO A 208 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" C4' DG T -15 " pdb=" C3' DG T -15 " pdb=" O3' DG T -15 " pdb=" P DG T -14 " ideal model delta sinusoidal sigma weight residual -140.00 28.89 -168.89 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" O4' A C -1 " pdb=" C1' A C -1 " pdb=" N9 A C -1 " pdb=" C4 A C -1 " ideal model delta sinusoidal sigma weight residual 70.00 1.19 68.81 1 2.00e+01 2.50e-03 1.53e+01 ... (remaining 7134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1560 0.069 - 0.139: 189 0.139 - 0.208: 5 0.208 - 0.277: 0 0.277 - 0.347: 1 Chirality restraints: 1755 Sorted by residual: chirality pdb=" CB ILE A1191 " pdb=" CA ILE A1191 " pdb=" CG1 ILE A1191 " pdb=" CG2 ILE A1191 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA GLN A 456 " pdb=" N GLN A 456 " pdb=" C GLN A 456 " pdb=" CB GLN A 456 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" C1' U C -15 " pdb=" O4' U C -15 " pdb=" C2' U C -15 " pdb=" N1 U C -15 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 1752 not shown) Planarity restraints: 1840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 869 " -0.042 5.00e-02 4.00e+02 6.20e-02 6.14e+00 pdb=" N PRO A 870 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 870 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 870 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 510 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 511 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 511 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 511 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U C -15 " -0.016 2.00e-02 2.50e+03 9.76e-03 2.14e+00 pdb=" N1 U C -15 " 0.024 2.00e-02 2.50e+03 pdb=" C2 U C -15 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U C -15 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U C -15 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U C -15 " -0.002 2.00e-02 2.50e+03 pdb=" O4 U C -15 " -0.003 2.00e-02 2.50e+03 pdb=" C5 U C -15 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U C -15 " 0.000 2.00e-02 2.50e+03 ... (remaining 1837 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 92 2.58 - 3.16: 9329 3.16 - 3.74: 18152 3.74 - 4.32: 25425 4.32 - 4.90: 40352 Nonbonded interactions: 93350 Sorted by model distance: nonbonded pdb=" OD2 ASP A 878 " pdb="MG MG A1303 " model vdw 2.004 2.170 nonbonded pdb=" OD1 ASP A 878 " pdb="MG MG A1303 " model vdw 2.046 2.170 nonbonded pdb=" OP2 A C -3 " pdb="MG MG C1401 " model vdw 2.089 2.170 nonbonded pdb=" O LEU A 902 " pdb=" OH TYR A 945 " model vdw 2.100 3.040 nonbonded pdb=" NH2 ARG A1179 " pdb="MG MG A1304 " model vdw 2.149 2.250 ... (remaining 93345 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.670 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: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.003 0.042 11889 Z= 0.233 Angle : 0.560 10.215 16333 Z= 0.406 Chirality : 0.043 0.347 1755 Planarity : 0.003 0.062 1840 Dihedral : 18.372 168.892 4861 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: 0.01 (0.25), residues: 1172 helix: 1.31 (0.23), residues: 521 sheet: -0.20 (0.53), residues: 111 loop : -1.27 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 716 TYR 0.024 0.001 TYR A1108 PHE 0.015 0.001 PHE A 978 TRP 0.008 0.001 TRP A1252 HIS 0.003 0.001 HIS A1222 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.23 (11889) covalent geometry : angle 0.55997 / 0.41 (16333) hydrogen bonds : bond 0.14395 / 9.54 ( 471) hydrogen bonds : angle 5.99063 / 4.19 ( 1310) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0727 time to fit residues: 7.6642 Evaluate side-chains 53 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 HIS A 122 ASN A 241 ASN A1170 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.218211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.174537 restraints weight = 12817.537| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 1.56 r_work: 0.3277 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.0643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11889 Z= 0.130 Angle : 0.517 6.695 16333 Z= 0.296 Chirality : 0.040 0.151 1755 Planarity : 0.003 0.054 1840 Dihedral : 18.355 167.248 2263 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.27 % Allowed : 4.22 % Favored : 95.51 % 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: 0.12 (0.25), residues: 1172 helix: 1.31 (0.23), residues: 521 sheet: -0.15 (0.52), residues: 109 loop : -1.10 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 44 TYR 0.018 0.001 TYR A 628 PHE 0.013 0.001 PHE A 978 TRP 0.011 0.001 TRP A 136 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (11889) covalent geometry : angle 0.51709 / 0.30 (16333) hydrogen bonds : bond 0.04122 / 2.64 ( 471) hydrogen bonds : angle 4.72777 / 3.32 ( 1310) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7801 (mt-10) REVERT: A 994 ASP cc_start: 0.8596 (m-30) cc_final: 0.8305 (m-30) REVERT: A 1072 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7401 (ptpt) outliers start: 3 outliers final: 2 residues processed: 67 average time/residue: 0.0773 time to fit residues: 8.1595 Evaluate side-chains 60 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 1072 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 65 optimal weight: 0.6980 chunk 68 optimal weight: 0.0570 chunk 30 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A 167 ASN A1170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.215869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.178775 restraints weight = 12900.242| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.37 r_work: 0.3340 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11889 Z= 0.175 Angle : 0.537 8.837 16333 Z= 0.301 Chirality : 0.041 0.153 1755 Planarity : 0.003 0.047 1840 Dihedral : 18.464 165.794 2263 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.55 % Allowed : 6.14 % Favored : 93.31 % 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: 0.07 (0.25), residues: 1172 helix: 1.27 (0.23), residues: 513 sheet: -0.14 (0.51), residues: 109 loop : -1.10 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.026 0.001 TYR A 628 PHE 0.013 0.001 PHE A 99 TRP 0.011 0.001 TRP A 136 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (11889) covalent geometry : angle 0.53657 / 0.30 (16333) hydrogen bonds : bond 0.04134 / 2.65 ( 471) hydrogen bonds : angle 4.57132 / 3.22 ( 1310) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1072 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7367 (ptpt) outliers start: 6 outliers final: 4 residues processed: 64 average time/residue: 0.0757 time to fit residues: 7.5384 Evaluate side-chains 60 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 1072 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 10 optimal weight: 0.9980 chunk 98 optimal weight: 0.0770 chunk 58 optimal weight: 0.5980 chunk 50 optimal weight: 0.0980 chunk 34 optimal weight: 20.0000 chunk 95 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1170 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.220644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.178273 restraints weight = 12838.358| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 1.45 r_work: 0.3263 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11889 Z= 0.111 Angle : 0.497 9.512 16333 Z= 0.280 Chirality : 0.039 0.139 1755 Planarity : 0.003 0.043 1840 Dihedral : 18.438 165.544 2263 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.64 % Allowed : 7.24 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.19 (0.25), residues: 1172 helix: 1.40 (0.24), residues: 508 sheet: -0.06 (0.51), residues: 109 loop : -1.06 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 879 TYR 0.017 0.001 TYR A 628 PHE 0.012 0.001 PHE A 508 TRP 0.010 0.001 TRP A 136 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (11889) covalent geometry : angle 0.49748 / 0.28 (16333) hydrogen bonds : bond 0.03574 / 2.26 ( 471) hydrogen bonds : angle 4.33338 / 3.04 ( 1310) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 503 MET cc_start: 0.3310 (OUTLIER) cc_final: 0.2547 (ptp) REVERT: A 1072 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7410 (ptpt) outliers start: 7 outliers final: 4 residues processed: 66 average time/residue: 0.0657 time to fit residues: 7.0256 Evaluate side-chains 64 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1178 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 54 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1170 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.215506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.173162 restraints weight = 12787.653| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 1.66 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11889 Z= 0.230 Angle : 0.595 14.699 16333 Z= 0.324 Chirality : 0.044 0.192 1755 Planarity : 0.004 0.042 1840 Dihedral : 18.604 163.408 2263 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.19 % Allowed : 8.16 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.01 (0.25), residues: 1172 helix: 1.17 (0.23), residues: 515 sheet: -0.08 (0.51), residues: 109 loop : -1.11 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.033 0.002 TYR A 628 PHE 0.015 0.001 PHE A 99 TRP 0.011 0.001 TRP A 578 HIS 0.006 0.001 HIS A 692 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.23 (11889) covalent geometry : angle 0.59523 / 0.32 (16333) hydrogen bonds : bond 0.04409 / 2.82 ( 471) hydrogen bonds : angle 4.51721 / 3.17 ( 1310) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1072 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6980 (ptpt) REVERT: A 1178 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7704 (mmt) outliers start: 13 outliers final: 6 residues processed: 66 average time/residue: 0.0712 time to fit residues: 7.7420 Evaluate side-chains 63 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1178 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 15 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1170 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.216612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.174942 restraints weight = 12835.893| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.47 r_work: 0.3285 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11889 Z= 0.168 Angle : 0.550 12.498 16333 Z= 0.302 Chirality : 0.041 0.231 1755 Planarity : 0.003 0.040 1840 Dihedral : 18.581 162.251 2263 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.92 % Allowed : 9.62 % Favored : 89.46 % 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: 0.06 (0.25), residues: 1172 helix: 1.20 (0.23), residues: 515 sheet: -0.04 (0.51), residues: 109 loop : -1.08 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 879 TYR 0.026 0.001 TYR A 628 PHE 0.014 0.001 PHE A 99 TRP 0.011 0.001 TRP A 136 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (11889) covalent geometry : angle 0.55023 / 0.30 (16333) hydrogen bonds : bond 0.03925 / 2.49 ( 471) hydrogen bonds : angle 4.40680 / 3.09 ( 1310) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1072 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7629 (ptpt) REVERT: A 1178 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8141 (mmt) outliers start: 10 outliers final: 6 residues processed: 62 average time/residue: 0.0802 time to fit residues: 7.9056 Evaluate side-chains 63 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1178 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 chunk 83 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 21 optimal weight: 0.0470 chunk 121 optimal weight: 40.0000 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1170 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.217817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.175247 restraints weight = 12789.322| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 1.59 r_work: 0.3279 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11889 Z= 0.133 Angle : 0.512 11.678 16333 Z= 0.286 Chirality : 0.040 0.142 1755 Planarity : 0.003 0.040 1840 Dihedral : 18.501 161.903 2263 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.73 % Allowed : 10.45 % Favored : 88.82 % 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: 0.14 (0.25), residues: 1172 helix: 1.31 (0.23), residues: 515 sheet: -0.51 (0.48), residues: 126 loop : -0.96 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 879 TYR 0.021 0.001 TYR A 628 PHE 0.014 0.001 PHE A 99 TRP 0.011 0.001 TRP A 136 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (11889) covalent geometry : angle 0.51185 / 0.29 (16333) hydrogen bonds : bond 0.03571 / 2.26 ( 471) hydrogen bonds : angle 4.25645 / 2.98 ( 1310) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1072 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7669 (ptpt) REVERT: A 1178 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8130 (mmt) outliers start: 8 outliers final: 6 residues processed: 64 average time/residue: 0.0759 time to fit residues: 7.7861 Evaluate side-chains 67 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1178 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 0.0870 chunk 53 optimal weight: 0.0020 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 103 optimal weight: 0.0770 chunk 3 optimal weight: 0.4980 chunk 43 optimal weight: 9.9990 overall best weight: 0.5326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1170 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.217112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.179457 restraints weight = 12682.476| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 1.42 r_work: 0.3334 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11889 Z= 0.113 Angle : 0.494 10.754 16333 Z= 0.278 Chirality : 0.039 0.140 1755 Planarity : 0.003 0.039 1840 Dihedral : 18.427 162.478 2263 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.82 % Allowed : 10.63 % Favored : 88.54 % 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: 0.23 (0.25), residues: 1172 helix: 1.42 (0.23), residues: 509 sheet: -0.44 (0.48), residues: 126 loop : -0.94 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 716 TYR 0.018 0.001 TYR A1078 PHE 0.012 0.001 PHE A 99 TRP 0.011 0.001 TRP A 136 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (11889) covalent geometry : angle 0.49399 / 0.28 (16333) hydrogen bonds : bond 0.03343 / 2.11 ( 471) hydrogen bonds : angle 4.11318 / 2.88 ( 1310) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1072 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7661 (ptpt) outliers start: 9 outliers final: 7 residues processed: 66 average time/residue: 0.0898 time to fit residues: 9.2212 Evaluate side-chains 66 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1131 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 0.0570 chunk 62 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 25 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1170 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.216131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.166674 restraints weight = 12649.991| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.75 r_work: 0.3267 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11889 Z= 0.138 Angle : 0.508 10.164 16333 Z= 0.285 Chirality : 0.040 0.141 1755 Planarity : 0.003 0.038 1840 Dihedral : 18.430 162.396 2263 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.82 % Allowed : 11.00 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.23 (0.25), residues: 1172 helix: 1.37 (0.23), residues: 516 sheet: -0.51 (0.48), residues: 126 loop : -0.87 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1077 TYR 0.023 0.001 TYR A 628 PHE 0.013 0.001 PHE A 99 TRP 0.009 0.001 TRP A 136 HIS 0.005 0.001 HIS A1222 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (11889) covalent geometry : angle 0.50807 / 0.28 (16333) hydrogen bonds : bond 0.03502 / 2.23 ( 471) hydrogen bonds : angle 4.14681 / 2.89 ( 1310) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1072 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7659 (ptpt) REVERT: A 1136 LYS cc_start: 0.7695 (mmtp) cc_final: 0.7372 (mmtt) outliers start: 9 outliers final: 7 residues processed: 67 average time/residue: 0.0846 time to fit residues: 8.8774 Evaluate side-chains 68 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 1072 LYS Chi-restraints excluded: chain A residue 1131 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 0.0870 chunk 69 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1170 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.216089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.160471 restraints weight = 12755.121| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.16 r_work: 0.3123 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11889 Z= 0.136 Angle : 0.509 10.007 16333 Z= 0.285 Chirality : 0.039 0.141 1755 Planarity : 0.003 0.038 1840 Dihedral : 18.422 162.198 2263 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.73 % Allowed : 11.27 % Favored : 87.99 % 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: 0.23 (0.25), residues: 1172 helix: 1.36 (0.23), residues: 516 sheet: -0.50 (0.48), residues: 126 loop : -0.87 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 879 TYR 0.022 0.001 TYR A 628 PHE 0.013 0.001 PHE A 99 TRP 0.009 0.001 TRP A 136 HIS 0.005 0.001 HIS A1222 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (11889) covalent geometry : angle 0.50899 / 0.28 (16333) hydrogen bonds : bond 0.03478 / 2.21 ( 471) hydrogen bonds : angle 4.12284 / 2.86 ( 1310) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1136 LYS cc_start: 0.7672 (mmtp) cc_final: 0.7343 (mmtt) outliers start: 8 outliers final: 7 residues processed: 65 average time/residue: 0.0763 time to fit residues: 7.8004 Evaluate side-chains 66 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 1131 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 79 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 30.0000 chunk 11 optimal weight: 0.3980 chunk 117 optimal weight: 3.9990 chunk 93 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 44 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4381 r_free = 0.4381 target = 0.218106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.175021 restraints weight = 12745.299| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.50 r_work: 0.3286 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11889 Z= 0.137 Angle : 0.510 9.772 16333 Z= 0.285 Chirality : 0.039 0.141 1755 Planarity : 0.003 0.038 1840 Dihedral : 18.411 162.074 2263 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.73 % Allowed : 11.18 % Favored : 88.08 % 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: 0.23 (0.25), residues: 1172 helix: 1.36 (0.23), residues: 516 sheet: -0.49 (0.48), residues: 126 loop : -0.87 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 879 TYR 0.023 0.001 TYR A 628 PHE 0.013 0.001 PHE A 99 TRP 0.009 0.001 TRP A 136 HIS 0.005 0.001 HIS A1222 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (11889) covalent geometry : angle 0.50999 / 0.28 (16333) hydrogen bonds : bond 0.03491 / 2.22 ( 471) hydrogen bonds : angle 4.11669 / 2.86 ( 1310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2022.91 seconds wall clock time: 35 minutes 31.29 seconds (2131.29 seconds total)