Starting phenix.real_space_refine on Fri Jul 3 01:35:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qwf_18694/07_2026/8qwf_18694.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qwf_18694/07_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_18694/07_2026/8qwf_18694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qwf_18694/07_2026/8qwf_18694.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qwf_18694/07_2026/8qwf_18694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qwf_18694/07_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-dev-6108/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: 1.98, per 1000 atoms: 0.17 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: 0.87 Conformation dependent library (CDL) restraints added in 376.3 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: 1.29 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: 2.61 Time building geometry restraints manager: 1.09 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: 16115 2.04 - 4.09: 200 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: 1593 0.069 - 0.139: 157 0.139 - 0.208: 4 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=" CB THR A 143 " pdb=" CA THR A 143 " pdb=" OG1 THR A 143 " pdb=" CG2 THR A 143 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.19e-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: 2.800 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.670 Find NCS groups from input model: 0.030 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.880 ------------------------------------------------------------------------------- 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= 0.231 Angle : 0.530 10.215 16333 Z= 0.377 Chirality : 0.040 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 0.00304 / 0.23 (11889) covalent geometry : angle 0.53042 / 0.38 (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 : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0871 time to fit residues: 9.2434 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 : 0.343 ------------------------------------------------------------------------------- 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 = 0.4383 r_free = 0.4383 target = 0.218267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.181007 restraints weight = 12830.267| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 1.31 r_work: 0.3406 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0598 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= 0.132 Angle : 0.513 6.831 16333 Z= 0.294 Chirality : 0.040 0.147 1755 Planarity : 0.003 0.055 1840 Dihedral : 18.364 166.612 2263 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.27 % Allowed : 4.31 % Favored : 95.42 % 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: 1.33 (0.24), residues: 520 sheet: -0.19 (0.51), residues: 111 loop : -1.12 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 833 TYR 0.018 0.001 TYR A 628 PHE 0.012 0.001 PHE A 978 TRP 0.010 0.001 TRP A 136 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (11889) covalent geometry : angle 0.51289 / 0.29 (16333) hydrogen bonds : bond 0.04211 / 2.70 ( 471) hydrogen bonds : angle 4.74805 / 3.33 ( 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 65 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 994 ASP cc_start: 0.8542 (m-30) cc_final: 0.8228 (m-30) REVERT: A 1072 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7294 (ptpt) outliers start: 3 outliers final: 2 residues processed: 65 average time/residue: 0.0790 time to fit residues: 8.0117 Evaluate side-chains 57 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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: 0.9980 chunk 68 optimal weight: 0.0370 chunk 30 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 95 optimal weight: 0.0000 chunk 57 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 overall best weight: 0.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A1170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.218014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.178955 restraints weight = 12913.013| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 1.46 r_work: 0.3404 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11889 Z= 0.122 Angle : 0.496 9.055 16333 Z= 0.282 Chirality : 0.039 0.155 1755 Planarity : 0.003 0.048 1840 Dihedral : 18.404 166.213 2263 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.73 % Allowed : 5.32 % Favored : 93.95 % 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: 0.20 (0.25), residues: 1172 helix: 1.42 (0.24), residues: 510 sheet: -0.11 (0.51), residues: 109 loop : -1.06 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 44 TYR 0.021 0.001 TYR A1078 PHE 0.012 0.001 PHE A 978 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 0.00246 / 0.12 (11889) covalent geometry : angle 0.49632 / 0.28 (16333) hydrogen bonds : bond 0.03787 / 2.41 ( 471) hydrogen bonds : angle 4.49045 / 3.15 ( 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 69 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 503 MET cc_start: 0.3395 (OUTLIER) cc_final: 0.2385 (ptp) REVERT: A 1072 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7355 (ptpt) outliers start: 8 outliers final: 3 residues processed: 67 average time/residue: 0.0737 time to fit residues: 7.6134 Evaluate side-chains 62 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 10 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 34 optimal weight: 20.0000 chunk 95 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A1170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.216899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.179443 restraints weight = 12782.070| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.45 r_work: 0.3389 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0981 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= 0.133 Angle : 0.505 9.289 16333 Z= 0.284 Chirality : 0.040 0.159 1755 Planarity : 0.003 0.044 1840 Dihedral : 18.455 165.529 2263 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.92 % Allowed : 6.78 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.25), residues: 1172 helix: 1.41 (0.23), residues: 511 sheet: -0.02 (0.51), residues: 109 loop : -1.03 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.022 0.001 TYR A 628 PHE 0.012 0.001 PHE A 99 TRP 0.009 0.001 TRP A 136 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (11889) covalent geometry : angle 0.50534 / 0.28 (16333) hydrogen bonds : bond 0.03657 / 2.32 ( 471) hydrogen bonds : angle 4.34034 / 3.05 ( 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 71 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1072 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7386 (ptpt) outliers start: 10 outliers final: 7 residues processed: 67 average time/residue: 0.0749 time to fit residues: 8.0433 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 : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 54 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A1170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.217098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.171656 restraints weight = 12812.568| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.04 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11889 Z= 0.204 Angle : 0.553 14.366 16333 Z= 0.305 Chirality : 0.042 0.169 1755 Planarity : 0.003 0.042 1840 Dihedral : 18.529 164.236 2263 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.10 % Allowed : 7.79 % Favored : 91.11 % 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: 0.16 (0.25), residues: 1172 helix: 1.28 (0.23), residues: 517 sheet: -0.02 (0.51), residues: 109 loop : -1.01 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.030 0.001 TYR A 628 PHE 0.014 0.001 PHE A 99 TRP 0.010 0.001 TRP A 136 HIS 0.005 0.001 HIS A1222 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (11889) covalent geometry : angle 0.55314 / 0.30 (16333) hydrogen bonds : bond 0.03979 / 2.53 ( 471) hydrogen bonds : angle 4.40881 / 3.10 ( 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 72 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1072 LYS cc_start: 0.7297 (OUTLIER) cc_final: 0.7051 (ptpt) outliers start: 12 outliers final: 6 residues processed: 68 average time/residue: 0.0792 time to fit residues: 8.6565 Evaluate side-chains 64 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 34 optimal weight: 30.0000 chunk 123 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A1170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.213656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.176828 restraints weight = 12838.679| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.47 r_work: 0.3270 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11889 Z= 0.275 Angle : 0.639 14.504 16333 Z= 0.346 Chirality : 0.045 0.215 1755 Planarity : 0.004 0.041 1840 Dihedral : 18.681 160.623 2263 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.28 % Allowed : 9.62 % Favored : 89.09 % 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: -0.17 (0.24), residues: 1172 helix: 0.97 (0.23), residues: 521 sheet: -0.11 (0.51), residues: 109 loop : -1.20 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 44 TYR 0.037 0.002 TYR A 628 PHE 0.016 0.002 PHE A 99 TRP 0.012 0.001 TRP A 578 HIS 0.005 0.002 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.28 (11889) covalent geometry : angle 0.63907 / 0.35 (16333) hydrogen bonds : bond 0.04631 / 2.94 ( 471) hydrogen bonds : angle 4.61443 / 3.24 ( 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 73 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1178 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8182 (mmt) outliers start: 14 outliers final: 6 residues processed: 69 average time/residue: 0.0780 time to fit residues: 8.3707 Evaluate side-chains 62 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 843 VAL 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: 0.9990 chunk 108 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 121 optimal weight: 40.0000 chunk 77 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A1170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.214631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.177067 restraints weight = 12761.689| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 1.37 r_work: 0.3399 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11889 Z= 0.143 Angle : 0.544 11.899 16333 Z= 0.302 Chirality : 0.041 0.241 1755 Planarity : 0.003 0.040 1840 Dihedral : 18.615 159.870 2263 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.64 % Allowed : 10.17 % Favored : 89.18 % 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: 0.00 (0.25), residues: 1172 helix: 1.15 (0.23), residues: 516 sheet: -0.08 (0.51), residues: 109 loop : -1.10 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 19 TYR 0.022 0.001 TYR A 628 PHE 0.014 0.001 PHE A 99 TRP 0.012 0.001 TRP A 136 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (11889) covalent geometry : angle 0.54386 / 0.30 (16333) hydrogen bonds : bond 0.03839 / 2.44 ( 471) hydrogen bonds : angle 4.43148 / 3.11 ( 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 65 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1136 LYS cc_start: 0.7361 (mmtp) cc_final: 0.7073 (mmtt) REVERT: A 1178 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8082 (mmt) outliers start: 7 outliers final: 4 residues processed: 62 average time/residue: 0.0781 time to fit residues: 7.5561 Evaluate side-chains 62 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 843 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: 4.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.4329 r_free = 0.4329 target = 0.212427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.179333 restraints weight = 12705.966| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 1.31 r_work: 0.3344 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11889 Z= 0.251 Angle : 0.616 15.822 16333 Z= 0.333 Chirality : 0.044 0.201 1755 Planarity : 0.003 0.039 1840 Dihedral : 18.653 157.408 2263 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.82 % Allowed : 10.45 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.24), residues: 1172 helix: 1.00 (0.23), residues: 515 sheet: -0.14 (0.51), residues: 109 loop : -1.21 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.035 0.002 TYR A 628 PHE 0.016 0.001 PHE A 99 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 0.00587 / 0.25 (11889) covalent geometry : angle 0.61599 / 0.33 (16333) hydrogen bonds : bond 0.04388 / 2.80 ( 471) hydrogen bonds : angle 4.56263 / 3.19 ( 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 67 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1136 LYS cc_start: 0.7513 (mmtp) cc_final: 0.7286 (mmtt) REVERT: A 1178 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8273 (mmt) outliers start: 9 outliers final: 7 residues processed: 62 average time/residue: 0.0780 time to fit residues: 7.6764 Evaluate side-chains 65 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 0.8980 chunk 74 optimal weight: 0.0270 chunk 20 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 54 optimal weight: 0.2980 chunk 70 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN A1170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.217789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.166524 restraints weight = 12705.896| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.66 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11889 Z= 0.119 Angle : 0.524 14.929 16333 Z= 0.291 Chirality : 0.039 0.176 1755 Planarity : 0.003 0.041 1840 Dihedral : 18.560 156.769 2263 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.64 % Allowed : 10.63 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.19 (0.23), residues: 514 sheet: -0.09 (0.51), residues: 109 loop : -1.04 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.022 0.001 TYR A1078 PHE 0.013 0.001 PHE A 99 TRP 0.013 0.001 TRP A 136 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (11889) covalent geometry : angle 0.52448 / 0.29 (16333) hydrogen bonds : bond 0.03556 / 2.25 ( 471) hydrogen bonds : angle 4.29024 / 3.00 ( 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 67 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1178 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7651 (mmt) outliers start: 7 outliers final: 5 residues processed: 63 average time/residue: 0.0812 time to fit residues: 8.0303 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 : 0.329 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 111 optimal weight: 0.1980 chunk 79 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 0.0010 chunk 69 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.0392 ------------------------------------------------------------------------------- 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 = 0.4351 r_free = 0.4351 target = 0.214782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.175070 restraints weight = 12784.275| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 1.52 r_work: 0.3363 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11889 Z= 0.152 Angle : 0.542 14.601 16333 Z= 0.298 Chirality : 0.040 0.175 1755 Planarity : 0.003 0.041 1840 Dihedral : 18.533 156.310 2263 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.64 % Allowed : 10.91 % Favored : 88.45 % 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: 1172 helix: 1.16 (0.23), residues: 516 sheet: -0.07 (0.51), residues: 109 loop : -1.03 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 19 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 A1222 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (11889) covalent geometry : angle 0.54156 / 0.30 (16333) hydrogen bonds : bond 0.03709 / 2.37 ( 471) hydrogen bonds : angle 4.29681 / 2.99 ( 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 64 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1178 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8049 (mmt) outliers start: 7 outliers final: 6 residues processed: 60 average time/residue: 0.0810 time to fit residues: 7.6550 Evaluate side-chains 62 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 79 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 30.0000 chunk 11 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 93 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 44 optimal weight: 0.0060 chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 overall best weight: 1.4200 ------------------------------------------------------------------------------- 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 = 0.4360 r_free = 0.4360 target = 0.215764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.167974 restraints weight = 12768.737| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.88 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11889 Z= 0.186 Angle : 0.563 14.257 16333 Z= 0.309 Chirality : 0.041 0.177 1755 Planarity : 0.003 0.042 1840 Dihedral : 18.575 154.273 2263 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.82 % Allowed : 10.82 % Favored : 88.36 % 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: -0.04 (0.25), residues: 1172 helix: 1.11 (0.23), residues: 516 sheet: -0.09 (0.51), residues: 109 loop : -1.12 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 879 TYR 0.029 0.002 TYR A 628 PHE 0.015 0.001 PHE A 99 TRP 0.010 0.001 TRP A 136 HIS 0.005 0.001 HIS A1222 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (11889) covalent geometry : angle 0.56329 / 0.31 (16333) hydrogen bonds : bond 0.03917 / 2.50 ( 471) hydrogen bonds : angle 4.34965 / 3.02 ( 1310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1778.33 seconds wall clock time: 31 minutes 22.01 seconds (1882.01 seconds total)