Starting phenix.real_space_refine on Fri Sep 11 13:44:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dmq_30767/09_2026/7dmq_30767.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dmq_30767/09_2026/7dmq_30767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7dmq_30767/09_2026/7dmq_30767.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dmq_30767/09_2026/7dmq_30767.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dmq_30767/09_2026/7dmq_30767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dmq_30767/09_2026/7dmq_30767.map" model { file = "/net/cci-nas-00/data/ceres_data/7dmq_30767/09_2026/7dmq_30767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dmq_30767/09_2026/7dmq_30767.cif" } resolution = 3.06 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= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 88 5.49 5 S 14 5.16 5 C 5705 2.51 5 N 1586 2.21 5 O 2051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9444 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 937, 7575 Classifications: {'peptide': 937} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 10, 'TRANS': 926} Chain breaks: 3 Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 274 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 18, 'ASP:plan': 8, 'PHE:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 7, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 175 Chain: "B" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1125 Classifications: {'RNAv2': 53} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 24, 'rna3p_pyr': 24} Link IDs: {'rna2p': 5, 'rna3p': 47} Chain: "C" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 744 Classifications: {'RNAv2': 35} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 17, 'rna3p_pyr': 15} Link IDs: {'rna2p': 2, 'rna3p': 32} Time building chain proxies: 2.20, per 1000 atoms: 0.23 Number of scatterers: 9444 At special positions: 0 Unit cell: (102.495, 110.246, 126.611, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 88 15.00 O 2051 8.00 N 1586 7.00 C 5705 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: 0.71 Conformation dependent library (CDL) restraints added in 258.2 milliseconds 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1826 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 3 sheets defined 54.3% alpha, 1.1% beta 26 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 342 through 346 removed outlier: 4.139A pdb=" N ILE A 345 " --> pdb=" O LYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 363 removed outlier: 3.763A pdb=" N PHE A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 376 removed outlier: 5.339A pdb=" N GLU A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 392 Processing helix chain 'A' and resid 400 through 412 Processing helix chain 'A' and resid 421 through 448 Processing helix chain 'A' and resid 471 through 493 removed outlier: 3.650A pdb=" N LEU A 490 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 512 through 524 removed outlier: 3.656A pdb=" N GLU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 572 removed outlier: 3.845A pdb=" N ILE A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 580 removed outlier: 3.997A pdb=" N ASN A 580 " --> pdb=" O ASN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 602 removed outlier: 3.766A pdb=" N ILE A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 596 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 628 removed outlier: 4.383A pdb=" N ILE A 621 " --> pdb=" O TYR A 617 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASN A 622 " --> pdb=" O ASN A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 656 Processing helix chain 'A' and resid 672 through 685 removed outlier: 3.701A pdb=" N VAL A 676 " --> pdb=" O SER A 672 " (cutoff:3.500A) Proline residue: A 678 - end of helix Processing helix chain 'A' and resid 699 through 718 removed outlier: 4.363A pdb=" N TYR A 708 " --> pdb=" O ASN A 704 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 718 " --> pdb=" O TYR A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 741 removed outlier: 4.262A pdb=" N GLU A 735 " --> pdb=" O ILE A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 789 removed outlier: 3.894A pdb=" N LYS A 787 " --> pdb=" O GLY A 783 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN A 788 " --> pdb=" O TYR A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 814 Processing helix chain 'A' and resid 834 through 845 removed outlier: 3.578A pdb=" N ILE A 842 " --> pdb=" O TYR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 867 removed outlier: 3.592A pdb=" N ASN A 857 " --> pdb=" O ASN A 853 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A 858 " --> pdb=" O LYS A 854 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 862 " --> pdb=" O ARG A 858 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 863 " --> pdb=" O PHE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 871 No H-bonds generated for 'chain 'A' and resid 869 through 871' Processing helix chain 'A' and resid 872 through 882 removed outlier: 3.763A pdb=" N ASP A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 877 " --> pdb=" O ASN A 873 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 879 " --> pdb=" O ILE A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 911 removed outlier: 3.964A pdb=" N GLN A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 906 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1033 Processing helix chain 'A' and resid 1060 through 1065 Processing helix chain 'A' and resid 1071 through 1077 removed outlier: 3.501A pdb=" N ILE A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY A1077 " --> pdb=" O ASP A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1084 Processing helix chain 'A' and resid 1093 through 1097 removed outlier: 3.537A pdb=" N GLY A1096 " --> pdb=" O ASN A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1111 Processing helix chain 'A' and resid 1122 through 1131 Processing helix chain 'A' and resid 1149 through 1170 removed outlier: 3.730A pdb=" N ASP A1155 " --> pdb=" O SER A1151 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A1167 " --> pdb=" O LYS A1163 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A1168 " --> pdb=" O LYS A1164 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A1169 " --> pdb=" O ILE A1165 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A1170 " --> pdb=" O ARG A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1209 removed outlier: 4.023A pdb=" N GLN A1191 " --> pdb=" O LYS A1187 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A1196 " --> pdb=" O MET A1192 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS A1200 " --> pdb=" O GLU A1196 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A1203 " --> pdb=" O MET A1199 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A1209 " --> pdb=" O GLY A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1245 through 1260 removed outlier: 3.620A pdb=" N TYR A1249 " --> pdb=" O ASP A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1281 Processing helix chain 'A' and resid 1284 through 1289 removed outlier: 3.627A pdb=" N ARG A1288 " --> pdb=" O PHE A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1305 removed outlier: 3.860A pdb=" N ASP A1301 " --> pdb=" O ALA A1297 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG A1302 " --> pdb=" O GLU A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1322 removed outlier: 3.718A pdb=" N PHE A1322 " --> pdb=" O TYR A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1327 removed outlier: 3.626A pdb=" N LYS A1326 " --> pdb=" O GLU A1323 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS A1327 " --> pdb=" O VAL A1324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1323 through 1327' Processing helix chain 'A' and resid 1332 through 1337 Processing helix chain 'A' and resid 1367 through 1381 removed outlier: 3.574A pdb=" N THR A1380 " --> pdb=" O ILE A1376 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A1381 " --> pdb=" O GLU A1377 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 533 through 535 Processing sheet with id=AA2, first strand: chain 'A' and resid 1216 through 1217 Processing sheet with id=AA3, first strand: chain 'A' and resid 1329 through 1331 294 hydrogen bonds defined for protein. 864 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2098 1.33 - 1.45: 2556 1.45 - 1.58: 4930 1.58 - 1.70: 174 1.70 - 1.82: 24 Bond restraints: 9782 Sorted by residual: bond pdb=" CB ASP A 381 " pdb=" CG ASP A 381 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.80e+00 bond pdb=" CB VAL A1287 " pdb=" CG1 VAL A1287 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.86e+00 bond pdb=" N ASP A 494 " pdb=" CA ASP A 494 " ideal model delta sigma weight residual 1.460 1.481 -0.021 1.42e-02 4.96e+03 2.21e+00 bond pdb=" CA ASP A 381 " pdb=" CB ASP A 381 " ideal model delta sigma weight residual 1.535 1.555 -0.020 1.37e-02 5.33e+03 2.19e+00 bond pdb=" C LEU A 677 " pdb=" N PRO A 678 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.28e-02 6.10e+03 2.16e+00 ... (remaining 9777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 12739 1.95 - 3.89: 725 3.89 - 5.84: 101 5.84 - 7.79: 24 7.79 - 9.73: 12 Bond angle restraints: 13601 Sorted by residual: angle pdb=" C ASN A 493 " pdb=" N ASP A 494 " pdb=" CA ASP A 494 " ideal model delta sigma weight residual 122.82 130.14 -7.32 1.42e+00 4.96e-01 2.66e+01 angle pdb=" C GLU A1265 " pdb=" N ASN A1266 " pdb=" CA ASN A1266 " ideal model delta sigma weight residual 121.54 130.56 -9.02 1.91e+00 2.74e-01 2.23e+01 angle pdb=" C ILE A 380 " pdb=" N ASP A 381 " pdb=" CA ASP A 381 " ideal model delta sigma weight residual 125.02 133.25 -8.23 1.76e+00 3.23e-01 2.18e+01 angle pdb=" C ASN A 897 " pdb=" N LEU A 898 " pdb=" CA LEU A 898 " ideal model delta sigma weight residual 121.26 128.04 -6.78 1.59e+00 3.96e-01 1.82e+01 angle pdb=" C ASN A 899 " pdb=" N LEU A 900 " pdb=" CA LEU A 900 " ideal model delta sigma weight residual 121.54 129.60 -8.06 1.91e+00 2.74e-01 1.78e+01 ... (remaining 13596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 5568 35.81 - 71.62: 199 71.62 - 107.43: 6 107.43 - 143.24: 0 143.24 - 179.05: 1 Dihedral angle restraints: 5774 sinusoidal: 2963 harmonic: 2811 Sorted by residual: dihedral pdb=" C4' G C 36 " pdb=" C3' G C 36 " pdb=" C2' G C 36 " pdb=" C1' G C 36 " ideal model delta sinusoidal sigma weight residual 36.34 -39.33 75.68 1 3.10e+00 1.04e-01 7.52e+02 dihedral pdb=" C4' C C 10 " pdb=" C3' C C 10 " pdb=" C2' C C 10 " pdb=" C1' C C 10 " ideal model delta sinusoidal sigma weight residual 36.34 -36.62 72.97 1 3.10e+00 1.04e-01 7.06e+02 dihedral pdb=" C4' G B 16 " pdb=" C3' G B 16 " pdb=" C2' G B 16 " pdb=" C1' G B 16 " ideal model delta sinusoidal sigma weight residual 36.35 -35.39 71.74 1 3.10e+00 1.04e-01 6.86e+02 ... (remaining 5771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1249 0.070 - 0.140: 216 0.140 - 0.209: 48 0.209 - 0.279: 83 0.279 - 0.349: 6 Chirality restraints: 1602 Sorted by residual: chirality pdb=" C2' G C 36 " pdb=" C3' G C 36 " pdb=" O2' G C 36 " pdb=" C1' G C 36 " both_signs ideal model delta sigma weight residual False -2.79 -2.44 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" C2' C C 10 " pdb=" C3' C C 10 " pdb=" O2' C C 10 " pdb=" C1' C C 10 " both_signs ideal model delta sigma weight residual False -2.79 -2.46 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" P A C 9 " pdb=" OP1 A C 9 " pdb=" OP2 A C 9 " pdb=" O5' A C 9 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 1599 not shown) Planarity restraints: 1412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A1053 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C LYS A1053 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS A1053 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN A1054 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 11 " 0.027 2.00e-02 2.50e+03 1.32e-02 3.92e+00 pdb=" N1 U C 11 " -0.022 2.00e-02 2.50e+03 pdb=" C2 U C 11 " -0.004 2.00e-02 2.50e+03 pdb=" O2 U C 11 " -0.001 2.00e-02 2.50e+03 pdb=" N3 U C 11 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U C 11 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U C 11 " 0.012 2.00e-02 2.50e+03 pdb=" C5 U C 11 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U C 11 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 825 " 0.009 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C THR A 825 " -0.033 2.00e-02 2.50e+03 pdb=" O THR A 825 " 0.013 2.00e-02 2.50e+03 pdb=" N SER A 826 " 0.011 2.00e-02 2.50e+03 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1747 2.77 - 3.30: 8593 3.30 - 3.84: 15905 3.84 - 4.37: 18841 4.37 - 4.90: 29240 Nonbonded interactions: 74326 Sorted by model distance: nonbonded pdb=" OH TYR A1180 " pdb=" OD2 ASP A1328 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR A 613 " pdb=" OD2 ASP A 835 " model vdw 2.306 3.040 nonbonded pdb=" OD1 ASP A1301 " pdb=" OH TYR A1318 " model vdw 2.316 3.040 nonbonded pdb=" O ASN A 649 " pdb=" OG1 THR A 652 " model vdw 2.326 3.040 nonbonded pdb=" O2' A B 10 " pdb=" OP2 U B 12 " model vdw 2.329 3.040 ... (remaining 74321 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: 1.030 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 10.930 Find NCS groups from input model: 0.040 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 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 : 0.005 0.056 9782 Z= 0.246 Angle : 1.035 9.732 13601 Z= 0.512 Chirality : 0.080 0.349 1602 Planarity : 0.005 0.045 1412 Dihedral : 15.423 179.054 3948 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 0.62 % Allowed : 7.18 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -5.19 (0.20), residues: 929 helix: -3.21 (0.15), residues: 542 sheet: -2.33 (2.15), residues: 10 loop : -3.70 (0.25), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 438 TYR 0.023 0.002 TYR A1024 PHE 0.032 0.003 PHE A 547 TRP 0.017 0.003 TRP A1186 HIS 0.004 0.002 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.25 ( 9782) covalent geometry : angle 1.03490 / 0.51 (13601) hydrogen bonds : bond 0.15711 / 9.20 ( 356) hydrogen bonds : angle 6.74732 / 4.67 ( 988) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 213 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 LYS cc_start: 0.8225 (pptt) cc_final: 0.7619 (pttt) REVERT: A 436 LYS cc_start: 0.7863 (tttt) cc_final: 0.7453 (tptp) REVERT: A 507 ARG cc_start: 0.7125 (tmm160) cc_final: 0.6744 (tpp-160) REVERT: A 567 LYS cc_start: 0.6289 (ttpt) cc_final: 0.5864 (tptm) REVERT: A 571 ASP cc_start: 0.6263 (m-30) cc_final: 0.5939 (m-30) REVERT: A 687 ASN cc_start: 0.7698 (t160) cc_final: 0.7419 (m-40) REVERT: A 699 GLU cc_start: 0.7894 (pp20) cc_final: 0.7548 (pp20) REVERT: A 734 GLN cc_start: 0.5937 (pp30) cc_final: 0.5619 (mt0) REVERT: A 776 LYS cc_start: 0.7587 (mttp) cc_final: 0.7382 (ttmm) REVERT: A 1182 ILE cc_start: 0.7354 (tp) cc_final: 0.7033 (tt) REVERT: A 1238 THR cc_start: 0.7542 (t) cc_final: 0.7281 (t) REVERT: A 1337 LYS cc_start: 0.6330 (ptmt) cc_final: 0.5887 (ptpp) REVERT: A 1354 LYS cc_start: 0.8317 (mmmt) cc_final: 0.7925 (mmmm) outliers start: 5 outliers final: 1 residues processed: 216 average time/residue: 0.1421 time to fit residues: 39.1700 Evaluate side-chains 109 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 464 ASN A 493 ASN A 563 ASN A 655 ASN A 687 ASN A 710 ASN A 815 ASN A 849 ASN A1062 ASN A1066 ASN A1204 ASN A1279 ASN A1305 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.196185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.158479 restraints weight = 11603.524| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.83 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9782 Z= 0.145 Angle : 0.811 11.483 13601 Z= 0.375 Chirality : 0.064 0.668 1602 Planarity : 0.004 0.066 1412 Dihedral : 14.811 170.523 2066 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 1.61 % Allowed : 12.75 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.78 (0.24), residues: 929 helix: -1.84 (0.20), residues: 542 sheet: -2.16 (2.12), residues: 10 loop : -3.48 (0.26), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1228 TYR 0.014 0.001 TYR A1162 PHE 0.020 0.002 PHE A1291 TRP 0.008 0.001 TRP A1186 HIS 0.003 0.001 HIS A1200 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 9782) covalent geometry : angle 0.81129 / 0.37 (13601) hydrogen bonds : bond 0.04835 / 2.97 ( 356) hydrogen bonds : angle 4.67833 / 3.26 ( 988) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 LYS cc_start: 0.7773 (pptt) cc_final: 0.7383 (pttp) REVERT: A 412 PHE cc_start: 0.2262 (t80) cc_final: 0.1934 (t80) REVERT: A 450 ARG cc_start: 0.6128 (ptt90) cc_final: 0.5624 (ppt170) REVERT: A 491 ARG cc_start: 0.7586 (tpt90) cc_final: 0.7337 (tpt90) REVERT: A 687 ASN cc_start: 0.7124 (t0) cc_final: 0.6726 (m-40) REVERT: A 1337 LYS cc_start: 0.6348 (ptmt) cc_final: 0.6144 (ptpp) outliers start: 13 outliers final: 5 residues processed: 120 average time/residue: 0.1172 time to fit residues: 19.0067 Evaluate side-chains 102 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1375 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN A1283 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.193947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.156895 restraints weight = 11604.876| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.74 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9782 Z= 0.150 Angle : 0.719 9.469 13601 Z= 0.336 Chirality : 0.056 0.393 1602 Planarity : 0.004 0.064 1412 Dihedral : 14.472 167.452 2066 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 2.60 % Allowed : 14.48 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.08 (0.25), residues: 929 helix: -1.25 (0.21), residues: 548 sheet: -2.54 (1.97), residues: 10 loop : -3.24 (0.27), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 438 TYR 0.014 0.002 TYR A 486 PHE 0.022 0.002 PHE A 404 TRP 0.004 0.001 TRP A1186 HIS 0.003 0.001 HIS A1200 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 9782) covalent geometry : angle 0.71935 / 0.34 (13601) hydrogen bonds : bond 0.04651 / 2.84 ( 356) hydrogen bonds : angle 4.40701 / 3.07 ( 988) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 LYS cc_start: 0.7748 (pptt) cc_final: 0.7409 (pttp) REVERT: A 1167 ASP cc_start: 0.5569 (OUTLIER) cc_final: 0.5318 (t0) REVERT: A 1337 LYS cc_start: 0.6429 (ptmt) cc_final: 0.6178 (ptpp) outliers start: 21 outliers final: 7 residues processed: 129 average time/residue: 0.1147 time to fit residues: 20.1480 Evaluate side-chains 107 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 738 LYS Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 1061 LYS Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1167 ASP Chi-restraints excluded: chain A residue 1375 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 10 optimal weight: 10.0000 chunk 78 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN A1175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.195620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.158959 restraints weight = 11705.022| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.60 r_work: 0.3622 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9782 Z= 0.124 Angle : 0.679 9.281 13601 Z= 0.317 Chirality : 0.053 0.317 1602 Planarity : 0.003 0.063 1412 Dihedral : 14.292 165.118 2066 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 2.23 % Allowed : 16.09 % Favored : 81.68 % 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: -2.49 (0.26), residues: 929 helix: -0.71 (0.22), residues: 541 sheet: -2.53 (1.96), residues: 10 loop : -3.04 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 685 TYR 0.013 0.001 TYR A 486 PHE 0.021 0.002 PHE A 357 TRP 0.008 0.001 TRP A1186 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 9782) covalent geometry : angle 0.67866 / 0.32 (13601) hydrogen bonds : bond 0.04156 / 2.53 ( 356) hydrogen bonds : angle 4.14589 / 2.91 ( 988) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 LYS cc_start: 0.8359 (pptt) cc_final: 0.7922 (pttp) REVERT: A 624 ILE cc_start: 0.8212 (mm) cc_final: 0.7830 (mt) REVERT: A 1167 ASP cc_start: 0.6527 (OUTLIER) cc_final: 0.6269 (t0) REVERT: A 1266 ASN cc_start: 0.7687 (p0) cc_final: 0.7417 (m-40) REVERT: A 1337 LYS cc_start: 0.6493 (ptmt) cc_final: 0.6104 (ptpp) outliers start: 18 outliers final: 9 residues processed: 119 average time/residue: 0.1175 time to fit residues: 18.8057 Evaluate side-chains 108 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 1061 LYS Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1167 ASP Chi-restraints excluded: chain A residue 1237 THR Chi-restraints excluded: chain A residue 1375 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 48 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 65 optimal weight: 0.0370 chunk 93 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 overall best weight: 1.2860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN A 655 ASN A 883 GLN A1062 ASN A1175 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.192305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.155319 restraints weight = 11848.669| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.62 r_work: 0.3573 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9782 Z= 0.155 Angle : 0.713 9.386 13601 Z= 0.330 Chirality : 0.054 0.301 1602 Planarity : 0.003 0.055 1412 Dihedral : 14.210 169.641 2066 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 2.97 % Allowed : 16.09 % Favored : 80.94 % 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: -2.36 (0.27), residues: 929 helix: -0.60 (0.22), residues: 551 sheet: -2.40 (1.97), residues: 10 loop : -3.07 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 685 TYR 0.013 0.002 TYR A 486 PHE 0.017 0.002 PHE A 357 TRP 0.002 0.001 TRP A1186 HIS 0.003 0.001 HIS A1200 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9782) covalent geometry : angle 0.71291 / 0.33 (13601) hydrogen bonds : bond 0.04524 / 2.80 ( 356) hydrogen bonds : angle 4.19531 / 2.95 ( 988) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 LYS cc_start: 0.8388 (pptt) cc_final: 0.7952 (pttp) REVERT: A 624 ILE cc_start: 0.8227 (mm) cc_final: 0.7904 (mt) REVERT: A 679 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7240 (mm-30) REVERT: A 790 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6902 (tm-30) REVERT: A 846 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7487 (mp) REVERT: A 1167 ASP cc_start: 0.6598 (OUTLIER) cc_final: 0.6335 (t0) REVERT: A 1266 ASN cc_start: 0.7748 (p0) cc_final: 0.7501 (m-40) REVERT: A 1337 LYS cc_start: 0.6572 (ptmt) cc_final: 0.6172 (ptpp) outliers start: 24 outliers final: 10 residues processed: 123 average time/residue: 0.1146 time to fit residues: 19.0534 Evaluate side-chains 112 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1061 LYS Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1167 ASP Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1237 THR Chi-restraints excluded: chain A residue 1375 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 53 optimal weight: 0.0670 chunk 79 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.194051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.157588 restraints weight = 11744.438| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 2.63 r_work: 0.3591 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9782 Z= 0.119 Angle : 0.690 8.903 13601 Z= 0.317 Chirality : 0.054 0.298 1602 Planarity : 0.004 0.065 1412 Dihedral : 14.259 170.271 2066 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 2.85 % Allowed : 16.34 % Favored : 80.82 % 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: -2.04 (0.27), residues: 929 helix: -0.26 (0.23), residues: 536 sheet: -2.30 (2.01), residues: 10 loop : -2.98 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 685 TYR 0.013 0.001 TYR A 486 PHE 0.018 0.001 PHE A 404 TRP 0.007 0.001 TRP A1186 HIS 0.003 0.001 HIS A 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 9782) covalent geometry : angle 0.69005 / 0.32 (13601) hydrogen bonds : bond 0.04155 / 2.55 ( 356) hydrogen bonds : angle 4.07158 / 2.86 ( 988) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 LYS cc_start: 0.8361 (pptt) cc_final: 0.7932 (pttp) REVERT: A 624 ILE cc_start: 0.8283 (mm) cc_final: 0.7984 (mt) REVERT: A 679 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7305 (mm-30) REVERT: A 790 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6734 (tm-30) REVERT: A 846 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7499 (mp) REVERT: A 1167 ASP cc_start: 0.6638 (OUTLIER) cc_final: 0.6382 (t0) REVERT: A 1266 ASN cc_start: 0.7804 (p0) cc_final: 0.7530 (m-40) REVERT: A 1337 LYS cc_start: 0.6531 (ptmt) cc_final: 0.6150 (ptpp) outliers start: 23 outliers final: 13 residues processed: 119 average time/residue: 0.1191 time to fit residues: 19.3500 Evaluate side-chains 111 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1167 ASP Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1375 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 79 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 62 optimal weight: 0.0870 chunk 56 optimal weight: 0.4980 chunk 93 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 35 optimal weight: 0.0570 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.0040 overall best weight: 0.2888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN A1175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.197002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.160982 restraints weight = 11669.044| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 2.61 r_work: 0.3640 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9782 Z= 0.104 Angle : 0.648 8.673 13601 Z= 0.298 Chirality : 0.052 0.296 1602 Planarity : 0.003 0.043 1412 Dihedral : 14.109 172.171 2066 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.23 % Allowed : 16.96 % Favored : 80.82 % 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: -1.75 (0.27), residues: 929 helix: 0.02 (0.23), residues: 540 sheet: -2.40 (2.00), residues: 10 loop : -2.95 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 685 TYR 0.011 0.001 TYR A 617 PHE 0.018 0.001 PHE A 401 TRP 0.011 0.001 TRP A1186 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 9782) covalent geometry : angle 0.64795 / 0.30 (13601) hydrogen bonds : bond 0.03768 / 2.28 ( 356) hydrogen bonds : angle 3.91573 / 2.74 ( 988) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 373 LYS cc_start: 0.8355 (pptt) cc_final: 0.7910 (pttp) REVERT: A 624 ILE cc_start: 0.8278 (mm) cc_final: 0.8043 (mt) REVERT: A 679 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7400 (mm-30) REVERT: A 790 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6682 (tm-30) REVERT: A 846 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7578 (mp) REVERT: A 1167 ASP cc_start: 0.6573 (OUTLIER) cc_final: 0.6340 (t0) REVERT: A 1192 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7599 (mmp) REVERT: A 1337 LYS cc_start: 0.6460 (ptmt) cc_final: 0.6066 (ptpp) outliers start: 18 outliers final: 8 residues processed: 124 average time/residue: 0.1168 time to fit residues: 19.5503 Evaluate side-chains 112 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1167 ASP Chi-restraints excluded: chain A residue 1192 MET Chi-restraints excluded: chain A residue 1219 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 22 optimal weight: 0.0970 chunk 0 optimal weight: 20.0000 chunk 42 optimal weight: 0.0470 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 67 optimal weight: 0.1980 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN A1175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.193467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.156782 restraints weight = 11740.355| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.58 r_work: 0.3583 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9782 Z= 0.136 Angle : 0.682 8.207 13601 Z= 0.313 Chirality : 0.053 0.295 1602 Planarity : 0.003 0.054 1412 Dihedral : 14.023 174.439 2066 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 2.60 % Allowed : 17.45 % Favored : 79.95 % 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: -1.69 (0.27), residues: 929 helix: 0.04 (0.23), residues: 542 sheet: -2.30 (2.01), residues: 10 loop : -2.90 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1207 TYR 0.012 0.001 TYR A 486 PHE 0.021 0.001 PHE A 404 TRP 0.002 0.001 TRP A1186 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 9782) covalent geometry : angle 0.68228 / 0.31 (13601) hydrogen bonds : bond 0.04219 / 2.60 ( 356) hydrogen bonds : angle 4.00473 / 2.82 ( 988) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 373 LYS cc_start: 0.8326 (pptt) cc_final: 0.7882 (pttp) REVERT: A 624 ILE cc_start: 0.8336 (mm) cc_final: 0.8070 (mt) REVERT: A 717 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7701 (mp) REVERT: A 790 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6771 (tm-30) REVERT: A 846 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7459 (mp) REVERT: A 1167 ASP cc_start: 0.6611 (OUTLIER) cc_final: 0.6357 (t0) REVERT: A 1192 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7656 (mmp) REVERT: A 1337 LYS cc_start: 0.6609 (ptmt) cc_final: 0.6230 (ptpp) outliers start: 21 outliers final: 9 residues processed: 112 average time/residue: 0.1107 time to fit residues: 16.9469 Evaluate side-chains 111 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1167 ASP Chi-restraints excluded: chain A residue 1192 MET Chi-restraints excluded: chain A residue 1237 THR Chi-restraints excluded: chain A residue 1375 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN A 690 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.190517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.154872 restraints weight = 11677.815| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.48 r_work: 0.3533 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9782 Z= 0.168 Angle : 0.732 8.002 13601 Z= 0.337 Chirality : 0.055 0.294 1602 Planarity : 0.004 0.061 1412 Dihedral : 14.007 176.497 2066 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 2.35 % Allowed : 18.19 % Favored : 79.46 % 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: -1.81 (0.27), residues: 929 helix: -0.09 (0.23), residues: 542 sheet: -2.42 (1.94), residues: 10 loop : -2.90 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 685 TYR 0.015 0.002 TYR A1318 PHE 0.016 0.002 PHE A 401 TRP 0.002 0.001 TRP A 865 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 ( 9782) covalent geometry : angle 0.73181 / 0.34 (13601) hydrogen bonds : bond 0.04631 / 2.88 ( 356) hydrogen bonds : angle 4.16944 / 2.95 ( 988) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 LYS cc_start: 0.8361 (pptt) cc_final: 0.8028 (pttp) REVERT: A 471 LYS cc_start: 0.7273 (mttp) cc_final: 0.6549 (mmmt) REVERT: A 624 ILE cc_start: 0.8285 (mm) cc_final: 0.8023 (mt) REVERT: A 790 GLU cc_start: 0.7316 (tm-30) cc_final: 0.7042 (tm-30) REVERT: A 846 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7488 (mp) REVERT: A 1167 ASP cc_start: 0.6646 (OUTLIER) cc_final: 0.6396 (t0) REVERT: A 1337 LYS cc_start: 0.6672 (ptmt) cc_final: 0.6276 (ptpp) outliers start: 19 outliers final: 10 residues processed: 120 average time/residue: 0.1052 time to fit residues: 17.1822 Evaluate side-chains 113 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1167 ASP Chi-restraints excluded: chain A residue 1237 THR Chi-restraints excluded: chain A residue 1375 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 16 optimal weight: 0.2980 chunk 83 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.193798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.156460 restraints weight = 11633.829| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 2.66 r_work: 0.3588 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9782 Z= 0.121 Angle : 0.683 8.271 13601 Z= 0.314 Chirality : 0.053 0.293 1602 Planarity : 0.003 0.063 1412 Dihedral : 13.977 176.189 2066 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 1.24 % Allowed : 19.55 % Favored : 79.21 % 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: -1.62 (0.27), residues: 929 helix: 0.12 (0.23), residues: 542 sheet: -2.40 (1.97), residues: 10 loop : -2.90 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 685 TYR 0.012 0.001 TYR A 617 PHE 0.022 0.001 PHE A 903 TRP 0.006 0.001 TRP A1186 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 9782) covalent geometry : angle 0.68317 / 0.31 (13601) hydrogen bonds : bond 0.04090 / 2.50 ( 356) hydrogen bonds : angle 3.99237 / 2.82 ( 988) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 LYS cc_start: 0.8332 (pptt) cc_final: 0.8008 (pttp) REVERT: A 443 LEU cc_start: 0.7456 (tt) cc_final: 0.7220 (mt) REVERT: A 624 ILE cc_start: 0.8195 (mm) cc_final: 0.7971 (mt) REVERT: A 790 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6914 (tm-30) REVERT: A 846 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7453 (mp) REVERT: A 1167 ASP cc_start: 0.6584 (OUTLIER) cc_final: 0.6334 (t0) REVERT: A 1337 LYS cc_start: 0.6715 (ptmt) cc_final: 0.6341 (ptpp) outliers start: 10 outliers final: 7 residues processed: 108 average time/residue: 0.1184 time to fit residues: 17.1842 Evaluate side-chains 105 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1167 ASP Chi-restraints excluded: chain A residue 1375 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 83 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 52 optimal weight: 0.0010 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.195562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.158747 restraints weight = 11667.987| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.67 r_work: 0.3616 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9782 Z= 0.114 Angle : 0.657 7.073 13601 Z= 0.302 Chirality : 0.052 0.289 1602 Planarity : 0.003 0.054 1412 Dihedral : 13.803 176.701 2066 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 1.24 % Allowed : 19.68 % Favored : 79.08 % 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: -1.32 (0.28), residues: 929 helix: 0.44 (0.23), residues: 535 sheet: -2.16 (2.06), residues: 10 loop : -2.85 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 685 TYR 0.010 0.001 TYR A 428 PHE 0.020 0.001 PHE A 903 TRP 0.007 0.001 TRP A1186 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 9782) covalent geometry : angle 0.65703 / 0.30 (13601) hydrogen bonds : bond 0.03899 / 2.38 ( 356) hydrogen bonds : angle 3.85701 / 2.72 ( 988) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2221.81 seconds wall clock time: 38 minutes 52.73 seconds (2332.73 seconds total)