Starting phenix.real_space_refine on Wed Mar 4 00:48:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dmq_30767/03_2026/7dmq_30767.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dmq_30767/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7dmq_30767/03_2026/7dmq_30767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dmq_30767/03_2026/7dmq_30767.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dmq_30767/03_2026/7dmq_30767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dmq_30767/03_2026/7dmq_30767.map" } 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-dev-5986/lib/python3.9/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: {'RNA': 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: {'RNA': 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: 2.38, per 1000 atoms: 0.25 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: 0.81 Conformation dependent library (CDL) restraints added in 407.0 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: 1.19 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: 1.82 Time building geometry restraints manager: 1.05 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: 12927 1.95 - 3.89: 562 3.89 - 5.84: 76 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: 5798 35.81 - 71.62: 215 71.62 - 107.43: 27 107.43 - 143.24: 1 143.24 - 179.05: 3 Dihedral angle restraints: 6044 sinusoidal: 3233 harmonic: 2811 Sorted by residual: dihedral pdb=" O4' U C 7 " pdb=" C1' U C 7 " pdb=" N1 U C 7 " pdb=" C2 U C 7 " ideal model delta sinusoidal sigma weight residual 200.00 47.72 152.28 1 1.50e+01 4.44e-03 8.04e+01 dihedral pdb=" O4' U C 3 " pdb=" C1' U C 3 " pdb=" N1 U C 3 " pdb=" C2 U C 3 " ideal model delta sinusoidal sigma weight residual 200.00 49.29 150.71 1 1.50e+01 4.44e-03 7.99e+01 dihedral pdb=" O4' U B 54 " pdb=" C1' U B 54 " pdb=" N1 U B 54 " pdb=" C2 U B 54 " ideal model delta sinusoidal sigma weight residual -160.00 -22.03 -137.97 1 1.50e+01 4.44e-03 7.44e+01 ... (remaining 6041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1162 0.053 - 0.107: 362 0.107 - 0.160: 58 0.160 - 0.213: 12 0.213 - 0.267: 8 Chirality restraints: 1602 Sorted by residual: chirality pdb=" CA ASP A 381 " pdb=" N ASP A 381 " pdb=" C ASP A 381 " pdb=" CB ASP A 381 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ASP A 494 " pdb=" N ASP A 494 " pdb=" C ASP A 494 " pdb=" CB ASP A 494 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ASN A1266 " pdb=" N ASN A1266 " pdb=" C ASN A1266 " pdb=" CB ASN A1266 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+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: 1.190 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: 0.030 Process input model: 11.380 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 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= 0.244 Angle : 0.958 9.732 13601 Z= 0.502 Chirality : 0.054 0.267 1602 Planarity : 0.005 0.045 1412 Dihedral : 17.295 179.054 4218 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 covalent geometry : bond 0.00534 ( 9782) covalent geometry : angle 0.95795 (13601) hydrogen bonds : bond 0.15711 ( 356) hydrogen bonds : angle 6.74732 ( 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 : 0.302 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: 0.1517 time to fit residues: 41.2338 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 : 0.313 ------------------------------------------------------------------------------- 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: 8.9990 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: 3.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.195637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.157662 restraints weight = 11529.702| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.79 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9782 Z= 0.131 Angle : 0.611 7.213 13601 Z= 0.322 Chirality : 0.041 0.202 1602 Planarity : 0.004 0.058 1412 Dihedral : 19.090 170.623 2336 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 1.73 % Allowed : 13.24 % Favored : 85.02 % 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: -3.79 (0.24), residues: 929 helix: -1.88 (0.19), residues: 545 sheet: -2.26 (2.08), residues: 10 loop : -3.44 (0.27), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1223 TYR 0.015 0.001 TYR A1162 PHE 0.019 0.002 PHE A1291 TRP 0.007 0.001 TRP A1186 HIS 0.003 0.001 HIS A1200 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9782) covalent geometry : angle 0.61142 (13601) hydrogen bonds : bond 0.04918 ( 356) hydrogen bonds : angle 4.63870 ( 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 126 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 LYS cc_start: 0.7797 (pptt) cc_final: 0.7406 (pttp) REVERT: A 412 PHE cc_start: 0.2215 (t80) cc_final: 0.1913 (t80) REVERT: A 450 ARG cc_start: 0.6110 (ptt90) cc_final: 0.5660 (ppt170) REVERT: A 491 ARG cc_start: 0.7624 (tpt90) cc_final: 0.7369 (tpt90) REVERT: A 687 ASN cc_start: 0.7182 (t0) cc_final: 0.6808 (m-40) outliers start: 14 outliers final: 5 residues processed: 122 average time/residue: 0.1216 time to fit residues: 19.8388 Evaluate side-chains 100 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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: 0.6980 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.195355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.162882 restraints weight = 11613.946| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.62 r_work: 0.3599 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9782 Z= 0.120 Angle : 0.555 6.485 13601 Z= 0.292 Chirality : 0.039 0.193 1602 Planarity : 0.003 0.063 1412 Dihedral : 18.801 171.179 2336 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 1.98 % Allowed : 14.48 % Favored : 83.54 % 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: -2.95 (0.25), residues: 929 helix: -1.13 (0.21), residues: 547 sheet: -2.43 (2.02), residues: 10 loop : -3.21 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1228 TYR 0.013 0.001 TYR A 486 PHE 0.020 0.002 PHE A 404 TRP 0.007 0.001 TRP A1186 HIS 0.003 0.001 HIS A1200 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9782) covalent geometry : angle 0.55497 (13601) hydrogen bonds : bond 0.04445 ( 356) hydrogen bonds : angle 4.25833 ( 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 128 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 373 LYS cc_start: 0.8334 (pptt) cc_final: 0.7846 (pttp) REVERT: A 378 PHE cc_start: 0.6664 (m-80) cc_final: 0.6455 (m-80) REVERT: A 432 TYR cc_start: 0.7940 (t80) cc_final: 0.7606 (t80) REVERT: A 790 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7143 (tm-30) REVERT: A 903 PHE cc_start: 0.6627 (m-10) cc_final: 0.6402 (m-10) outliers start: 16 outliers final: 6 residues processed: 124 average time/residue: 0.1141 time to fit residues: 18.8279 Evaluate side-chains 100 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU 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 1091 LEU 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: 8.9990 chunk 78 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 HIS ** 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 = 0.4437 r_free = 0.4437 target = 0.192312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.154969 restraints weight = 11653.404| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.65 r_work: 0.3583 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9782 Z= 0.148 Angle : 0.581 7.173 13601 Z= 0.304 Chirality : 0.040 0.188 1602 Planarity : 0.003 0.058 1412 Dihedral : 18.664 174.175 2336 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 2.85 % Allowed : 15.59 % Favored : 81.56 % 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: -2.51 (0.26), residues: 929 helix: -0.75 (0.22), residues: 544 sheet: -2.56 (1.93), residues: 10 loop : -3.04 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 685 TYR 0.015 0.002 TYR A 486 PHE 0.015 0.002 PHE A 357 TRP 0.002 0.001 TRP A1186 HIS 0.003 0.001 HIS A1200 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9782) covalent geometry : angle 0.58064 (13601) hydrogen bonds : bond 0.04676 ( 356) hydrogen bonds : angle 4.21961 ( 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 125 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 373 LYS cc_start: 0.8331 (pptt) cc_final: 0.7893 (pttp) REVERT: A 378 PHE cc_start: 0.6705 (m-80) cc_final: 0.6454 (m-80) REVERT: A 790 GLU cc_start: 0.7358 (tm-30) cc_final: 0.7025 (tm-30) REVERT: A 846 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7529 (mp) REVERT: A 1266 ASN cc_start: 0.7702 (p0) cc_final: 0.7452 (m-40) outliers start: 23 outliers final: 12 residues processed: 118 average time/residue: 0.1155 time to fit residues: 18.0328 Evaluate side-chains 106 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 698 THR 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 1061 LYS Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1091 LEU 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: 6.9990 chunk 62 optimal weight: 0.0000 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 69 optimal weight: 0.0980 chunk 47 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 ASN A1062 ASN A1175 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.195936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.160266 restraints weight = 11837.823| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 2.64 r_work: 0.3640 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9782 Z= 0.105 Angle : 0.537 7.598 13601 Z= 0.277 Chirality : 0.038 0.188 1602 Planarity : 0.003 0.049 1412 Dihedral : 18.577 178.346 2336 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.23 % Allowed : 17.45 % Favored : 80.32 % 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: -2.06 (0.27), residues: 929 helix: -0.30 (0.23), residues: 541 sheet: -2.52 (1.95), residues: 10 loop : -2.98 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 685 TYR 0.012 0.001 TYR A 617 PHE 0.015 0.001 PHE A 404 TRP 0.010 0.001 TRP A1186 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 9782) covalent geometry : angle 0.53667 (13601) hydrogen bonds : bond 0.04036 ( 356) hydrogen bonds : angle 3.97641 ( 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 125 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 LYS cc_start: 0.8334 (pptt) cc_final: 0.7886 (pttp) REVERT: A 624 ILE cc_start: 0.8278 (mm) cc_final: 0.7995 (mt) REVERT: A 679 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7174 (mm-30) REVERT: A 790 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6807 (tm-30) REVERT: A 1063 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7768 (tt) REVERT: A 1266 ASN cc_start: 0.7692 (p0) cc_final: 0.7466 (m-40) outliers start: 18 outliers final: 9 residues processed: 121 average time/residue: 0.1134 time to fit residues: 18.3085 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 : 0.320 ------------------------------------------------------------------------------- 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 638 LEU Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 1061 LYS Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1219 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 53 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.196118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.159887 restraints weight = 11751.604| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 2.62 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9782 Z= 0.103 Angle : 0.518 6.532 13601 Z= 0.269 Chirality : 0.038 0.197 1602 Planarity : 0.003 0.046 1412 Dihedral : 18.481 176.075 2336 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.85 % Allowed : 16.58 % Favored : 80.57 % 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: -1.72 (0.27), residues: 929 helix: 0.06 (0.23), residues: 540 sheet: -2.44 (1.98), residues: 10 loop : -2.96 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 685 TYR 0.012 0.001 TYR A 617 PHE 0.019 0.001 PHE A 357 TRP 0.007 0.001 TRP A1186 HIS 0.003 0.001 HIS A1200 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 9782) covalent geometry : angle 0.51832 (13601) hydrogen bonds : bond 0.03912 ( 356) hydrogen bonds : angle 3.89268 ( 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 127 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 LYS cc_start: 0.7524 (pptt) cc_final: 0.7235 (pttp) REVERT: A 624 ILE cc_start: 0.8305 (mm) cc_final: 0.8070 (mt) REVERT: A 679 GLU cc_start: 0.6605 (mm-30) cc_final: 0.6346 (mm-30) REVERT: A 790 GLU cc_start: 0.6592 (tm-30) cc_final: 0.6236 (tm-30) REVERT: A 846 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7321 (mp) REVERT: A 898 LEU cc_start: 0.5841 (OUTLIER) cc_final: 0.5607 (tp) outliers start: 23 outliers final: 10 residues processed: 122 average time/residue: 0.1117 time to fit residues: 18.4071 Evaluate side-chains 109 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 745 GLU 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 1219 THR 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: 4.9990 chunk 53 optimal weight: 0.0020 chunk 1 optimal weight: 0.0870 chunk 80 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 35 optimal weight: 0.0060 chunk 54 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 overall best weight: 0.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.199554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.164043 restraints weight = 11787.822| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 2.61 r_work: 0.3691 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9782 Z= 0.094 Angle : 0.507 7.960 13601 Z= 0.261 Chirality : 0.038 0.191 1602 Planarity : 0.003 0.043 1412 Dihedral : 18.348 168.074 2336 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 1.98 % Allowed : 18.44 % Favored : 79.58 % 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: -1.40 (0.28), residues: 929 helix: 0.39 (0.24), residues: 539 sheet: None (None), residues: 0 loop : -2.95 (0.27), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 685 TYR 0.011 0.001 TYR A 617 PHE 0.015 0.001 PHE A 357 TRP 0.011 0.001 TRP A1186 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 9782) covalent geometry : angle 0.50741 (13601) hydrogen bonds : bond 0.03628 ( 356) hydrogen bonds : angle 3.76522 ( 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 126 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 LYS cc_start: 0.8368 (pptt) cc_final: 0.7948 (pttp) REVERT: A 624 ILE cc_start: 0.8239 (mm) cc_final: 0.7977 (mt) REVERT: A 717 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7730 (mp) REVERT: A 790 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6679 (tm-30) REVERT: A 846 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7479 (mp) REVERT: A 898 LEU cc_start: 0.5617 (OUTLIER) cc_final: 0.5271 (tp) outliers start: 16 outliers final: 7 residues processed: 122 average time/residue: 0.1149 time to fit residues: 18.9251 Evaluate side-chains 109 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 846 LEU 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 1219 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 22 optimal weight: 0.0030 chunk 0 optimal weight: 20.0000 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 76 optimal weight: 0.0050 chunk 80 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.7606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN A 883 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.195791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.160822 restraints weight = 11771.299| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.49 r_work: 0.3622 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9782 Z= 0.111 Angle : 0.533 6.514 13601 Z= 0.273 Chirality : 0.039 0.223 1602 Planarity : 0.003 0.051 1412 Dihedral : 18.275 163.017 2336 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 1.86 % Allowed : 19.31 % Favored : 78.84 % 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: -1.33 (0.28), residues: 929 helix: 0.44 (0.24), residues: 536 sheet: -2.37 (2.01), residues: 10 loop : -2.88 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 685 TYR 0.010 0.001 TYR A 617 PHE 0.015 0.001 PHE A 357 TRP 0.003 0.001 TRP A1186 HIS 0.002 0.001 HIS A 483 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9782) covalent geometry : angle 0.53276 (13601) hydrogen bonds : bond 0.03920 ( 356) hydrogen bonds : angle 3.81789 ( 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 111 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 373 LYS cc_start: 0.8387 (pptt) cc_final: 0.7941 (pttp) REVERT: A 443 LEU cc_start: 0.7221 (tt) cc_final: 0.6912 (tp) REVERT: A 624 ILE cc_start: 0.8276 (mm) cc_final: 0.7961 (mt) REVERT: A 717 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7677 (mp) REVERT: A 790 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6902 (tm-30) REVERT: A 846 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7436 (mp) REVERT: A 898 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.5950 (tp) outliers start: 15 outliers final: 9 residues processed: 107 average time/residue: 0.1141 time to fit residues: 16.5545 Evaluate side-chains 107 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU 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 717 LEU 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 1061 LYS Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1219 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: 0.7980 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4429 r_free = 0.4429 target = 0.191942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.155192 restraints weight = 11686.282| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.58 r_work: 0.3571 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4373 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= 0.143 Angle : 0.583 8.182 13601 Z= 0.298 Chirality : 0.041 0.222 1602 Planarity : 0.003 0.056 1412 Dihedral : 18.292 160.428 2336 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 1.86 % Allowed : 19.55 % Favored : 78.59 % 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: -1.46 (0.28), residues: 929 helix: 0.26 (0.23), residues: 542 sheet: -2.49 (1.93), residues: 10 loop : -2.84 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 685 TYR 0.012 0.001 TYR A1318 PHE 0.017 0.002 PHE A 903 TRP 0.002 0.001 TRP A1186 HIS 0.003 0.001 HIS A1200 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9782) covalent geometry : angle 0.58291 (13601) hydrogen bonds : bond 0.04397 ( 356) hydrogen bonds : angle 3.96593 ( 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 114 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 LYS cc_start: 0.8315 (pptt) cc_final: 0.7950 (pttp) REVERT: A 443 LEU cc_start: 0.7201 (tt) cc_final: 0.6952 (tp) REVERT: A 624 ILE cc_start: 0.8380 (mm) cc_final: 0.8102 (mt) REVERT: A 717 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7697 (mp) REVERT: A 768 LYS cc_start: 0.7759 (mmtm) cc_final: 0.7372 (mptt) REVERT: A 790 GLU cc_start: 0.7334 (tm-30) cc_final: 0.7004 (tm-30) REVERT: A 846 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7460 (mp) outliers start: 15 outliers final: 9 residues processed: 110 average time/residue: 0.1017 time to fit residues: 15.1660 Evaluate side-chains 107 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU 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 717 LEU 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 1061 LYS Chi-restraints excluded: chain A residue 1091 LEU 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: 4.9990 chunk 55 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.192336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.155416 restraints weight = 11656.537| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.60 r_work: 0.3576 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4504 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= 0.135 Angle : 0.577 7.530 13601 Z= 0.295 Chirality : 0.041 0.242 1602 Planarity : 0.003 0.062 1412 Dihedral : 18.265 158.978 2336 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 1.49 % Allowed : 20.54 % Favored : 77.97 % 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: -1.46 (0.28), residues: 929 helix: 0.25 (0.23), residues: 541 sheet: -2.44 (1.96), residues: 10 loop : -2.81 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 685 TYR 0.011 0.001 TYR A 617 PHE 0.026 0.002 PHE A 404 TRP 0.002 0.001 TRP A 865 HIS 0.003 0.001 HIS A1200 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9782) covalent geometry : angle 0.57734 (13601) hydrogen bonds : bond 0.04223 ( 356) hydrogen bonds : angle 3.95381 ( 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 109 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 373 LYS cc_start: 0.8347 (pptt) cc_final: 0.7891 (pttp) REVERT: A 443 LEU cc_start: 0.7218 (tt) cc_final: 0.6972 (tp) REVERT: A 608 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.5862 (tpp-160) REVERT: A 624 ILE cc_start: 0.8272 (mm) cc_final: 0.8016 (mt) REVERT: A 717 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7737 (mp) REVERT: A 768 LYS cc_start: 0.7754 (mmtm) cc_final: 0.7367 (mptt) REVERT: A 790 GLU cc_start: 0.7398 (tm-30) cc_final: 0.7072 (tm-30) REVERT: A 846 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7452 (mp) outliers start: 12 outliers final: 9 residues processed: 105 average time/residue: 0.1203 time to fit residues: 16.9999 Evaluate side-chains 107 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 674 SER 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 898 LEU Chi-restraints excluded: chain A residue 1061 LYS Chi-restraints excluded: chain A residue 1091 LEU 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: 0.8980 chunk 6 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 82 optimal weight: 0.0870 chunk 52 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4441 r_free = 0.4441 target = 0.193115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.156364 restraints weight = 11674.429| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.61 r_work: 0.3594 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9782 Z= 0.113 Angle : 0.570 7.225 13601 Z= 0.291 Chirality : 0.040 0.255 1602 Planarity : 0.003 0.064 1412 Dihedral : 18.275 158.856 2336 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 1.86 % Allowed : 20.05 % Favored : 78.09 % 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: -1.37 (0.28), residues: 929 helix: 0.33 (0.23), residues: 541 sheet: -2.45 (1.95), residues: 10 loop : -2.80 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1223 TYR 0.012 0.001 TYR A 617 PHE 0.023 0.001 PHE A 404 TRP 0.004 0.001 TRP A1186 HIS 0.003 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9782) covalent geometry : angle 0.56982 (13601) hydrogen bonds : bond 0.04068 ( 356) hydrogen bonds : angle 3.91439 ( 988) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2243.08 seconds wall clock time: 39 minutes 12.34 seconds (2352.34 seconds total)