Starting phenix.real_space_refine on Wed Feb 4 14:09:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lge_63063/02_2026/9lge_63063_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lge_63063/02_2026/9lge_63063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lge_63063/02_2026/9lge_63063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lge_63063/02_2026/9lge_63063.map" model { file = "/net/cci-nas-00/data/ceres_data/9lge_63063/02_2026/9lge_63063_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lge_63063/02_2026/9lge_63063_neut.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 57 5.16 5 C 6998 2.51 5 N 1789 2.21 5 O 1931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10783 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1349, 10719 Classifications: {'peptide': 1349} Link IDs: {'PTRANS': 48, 'TRANS': 1300} Chain breaks: 10 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.62, per 1000 atoms: 0.24 Number of scatterers: 10783 At special positions: 0 Unit cell: (75, 111, 144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 57 16.00 P 6 15.00 Mg 2 11.99 O 1931 8.00 N 1789 7.00 C 6998 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: 0.95 Conformation dependent library (CDL) restraints added in 479.6 milliseconds 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2554 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 71.4% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 removed outlier: 3.653A pdb=" N THR A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 60 removed outlier: 3.960A pdb=" N LEU A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL A 39 " --> pdb=" O ASN A 35 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 51 - end of helix removed outlier: 3.866A pdb=" N LEU A 55 " --> pdb=" O PRO A 51 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 56 " --> pdb=" O PHE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 94 removed outlier: 3.696A pdb=" N LEU A 89 " --> pdb=" O CYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 130 removed outlier: 3.578A pdb=" N VAL A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 135 through 160 Processing helix chain 'A' and resid 171 through 191 removed outlier: 3.543A pdb=" N PHE A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 214 through 220 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 224 through 234 Processing helix chain 'A' and resid 249 through 268 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 312 through 326 removed outlier: 3.746A pdb=" N VAL A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Proline residue: A 323 - end of helix Processing helix chain 'A' and resid 326 through 353 removed outlier: 3.723A pdb=" N LEU A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 359 through 410 removed outlier: 3.852A pdb=" N GLY A 363 " --> pdb=" O PRO A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 419 through 429 Processing helix chain 'A' and resid 430 through 441 removed outlier: 3.609A pdb=" N PHE A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 463 Processing helix chain 'A' and resid 465 through 511 removed outlier: 4.000A pdb=" N GLY A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Proline residue: A 478 - end of helix Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'A' and resid 520 through 570 Proline residue: A 557 - end of helix removed outlier: 3.533A pdb=" N THR A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 594 removed outlier: 3.509A pdb=" N SER A 585 " --> pdb=" O LYS A 581 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU A 588 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE A 594 " --> pdb=" O ASN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 597 No H-bonds generated for 'chain 'A' and resid 595 through 597' Processing helix chain 'A' and resid 598 through 621 removed outlier: 3.761A pdb=" N SER A 604 " --> pdb=" O PRO A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 630 Processing helix chain 'A' and resid 683 through 692 Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 733 through 744 removed outlier: 3.516A pdb=" N ALA A 739 " --> pdb=" O ARG A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 769 through 784 Processing helix chain 'A' and resid 799 through 810 Processing helix chain 'A' and resid 851 through 856 Processing helix chain 'A' and resid 860 through 869 Processing helix chain 'A' and resid 958 through 970 removed outlier: 3.845A pdb=" N TYR A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 998 Processing helix chain 'A' and resid 1010 through 1058 removed outlier: 3.615A pdb=" N THR A1028 " --> pdb=" O SER A1024 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A1037 " --> pdb=" O SER A1033 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A1038 " --> pdb=" O MET A1034 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A1049 " --> pdb=" O ARG A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1066 removed outlier: 3.551A pdb=" N PHE A1063 " --> pdb=" O PRO A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1077 Processing helix chain 'A' and resid 1077 through 1084 Processing helix chain 'A' and resid 1084 through 1110 removed outlier: 3.535A pdb=" N GLN A1088 " --> pdb=" O SER A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1116 removed outlier: 3.647A pdb=" N VAL A1116 " --> pdb=" O MET A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1160 removed outlier: 4.297A pdb=" N SER A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLN A1138 " --> pdb=" O ALA A1134 " (cutoff:3.500A) Proline residue: A1149 - end of helix Processing helix chain 'A' and resid 1160 through 1168 Processing helix chain 'A' and resid 1169 through 1220 Proline residue: A1190 - end of helix removed outlier: 4.300A pdb=" N PHE A1212 " --> pdb=" O CYS A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1265 removed outlier: 3.880A pdb=" N GLN A1238 " --> pdb=" O SER A1234 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A1249 " --> pdb=" O TRP A1245 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A1258 " --> pdb=" O GLU A1254 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 removed outlier: 3.649A pdb=" N THR A1336 " --> pdb=" O LYS A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1367 Processing helix chain 'A' and resid 1383 through 1388 Processing helix chain 'A' and resid 1394 through 1404 Processing helix chain 'A' and resid 1407 through 1414 Processing helix chain 'A' and resid 1416 through 1419 Processing helix chain 'A' and resid 1423 through 1427 removed outlier: 3.951A pdb=" N GLU A1427 " --> pdb=" O GLU A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1446 Processing helix chain 'A' and resid 1460 through 1475 Processing helix chain 'A' and resid 1486 through 1490 Processing helix chain 'A' and resid 1509 through 1517 Processing helix chain 'A' and resid 1518 through 1527 Processing sheet with id=AA1, first strand: chain 'A' and resid 664 through 669 removed outlier: 5.370A pdb=" N ILE A 664 " --> pdb=" O ASN A 648 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 651 through 652 Processing sheet with id=AA3, first strand: chain 'A' and resid 708 through 711 removed outlier: 6.585A pdb=" N TYR A 789 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL A 825 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU A 791 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL A 674 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU A 673 " --> pdb=" O VAL A 837 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE A 839 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA A 675 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N MET A 841 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL A 677 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 848 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER A 842 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ILE A 846 " --> pdb=" O SER A 842 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1370 through 1372 removed outlier: 7.019A pdb=" N VAL A1322 " --> pdb=" O THR A1482 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LYS A1321 " --> pdb=" O ARG A1495 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE A1497 " --> pdb=" O LYS A1321 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLY A1323 " --> pdb=" O ILE A1497 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU A1499 " --> pdb=" O GLY A1323 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL A1325 " --> pdb=" O LEU A1499 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU A1506 " --> pdb=" O VAL A1498 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1351 through 1352 Processing sheet with id=AA6, first strand: chain 'A' and resid 1381 through 1382 705 hydrogen bonds defined for protein. 2070 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1689 1.31 - 1.44: 2980 1.44 - 1.56: 6250 1.56 - 1.69: 10 1.69 - 1.81: 93 Bond restraints: 11022 Sorted by residual: bond pdb=" C TRP A1245 " pdb=" O TRP A1245 " ideal model delta sigma weight residual 1.235 1.186 0.050 1.33e-02 5.65e+03 1.41e+01 bond pdb=" C ARG A 218 " pdb=" O ARG A 218 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.29e-02 6.01e+03 1.10e+01 bond pdb=" N ILE A 224 " pdb=" CA ILE A 224 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.09e-02 8.42e+03 1.09e+01 bond pdb=" N ILE A 576 " pdb=" CA ILE A 576 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.24e-02 6.50e+03 9.56e+00 bond pdb=" N ILE A 115 " pdb=" CA ILE A 115 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.29e+00 ... (remaining 11017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 14569 2.44 - 4.88: 374 4.88 - 7.33: 25 7.33 - 9.77: 3 9.77 - 12.21: 1 Bond angle restraints: 14972 Sorted by residual: angle pdb=" N ILE A1209 " pdb=" CA ILE A1209 " pdb=" C ILE A1209 " ideal model delta sigma weight residual 113.71 101.50 12.21 9.50e-01 1.11e+00 1.65e+02 angle pdb=" PB ATP A1603 " pdb=" O3B ATP A1603 " pdb=" PG ATP A1603 " ideal model delta sigma weight residual 139.87 130.86 9.01 1.00e+00 1.00e+00 8.12e+01 angle pdb=" C5' ATP A1603 " pdb=" O5' ATP A1603 " pdb=" PA ATP A1603 " ideal model delta sigma weight residual 121.27 113.28 7.99 1.00e+00 1.00e+00 6.38e+01 angle pdb=" PB ATP A1601 " pdb=" O3B ATP A1601 " pdb=" PG ATP A1601 " ideal model delta sigma weight residual 139.87 132.20 7.67 1.00e+00 1.00e+00 5.88e+01 angle pdb=" N CYS A1208 " pdb=" CA CYS A1208 " pdb=" C CYS A1208 " ideal model delta sigma weight residual 112.59 105.39 7.20 1.22e+00 6.72e-01 3.49e+01 ... (remaining 14967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5750 17.94 - 35.88: 631 35.88 - 53.83: 147 53.83 - 71.77: 34 71.77 - 89.71: 10 Dihedral angle restraints: 6572 sinusoidal: 2634 harmonic: 3938 Sorted by residual: dihedral pdb=" CA VAL A 429 " pdb=" C VAL A 429 " pdb=" N ASP A 430 " pdb=" CA ASP A 430 " ideal model delta harmonic sigma weight residual 180.00 156.32 23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ASP A1395 " pdb=" CB ASP A1395 " pdb=" CG ASP A1395 " pdb=" OD1 ASP A1395 " ideal model delta sinusoidal sigma weight residual -30.00 -89.17 59.17 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP A1375 " pdb=" CB ASP A1375 " pdb=" CG ASP A1375 " pdb=" OD1 ASP A1375 " ideal model delta sinusoidal sigma weight residual -30.00 -87.77 57.77 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 6569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1301 0.055 - 0.109: 307 0.109 - 0.163: 100 0.163 - 0.218: 31 0.218 - 0.272: 2 Chirality restraints: 1741 Sorted by residual: chirality pdb=" CA ILE A1209 " pdb=" N ILE A1209 " pdb=" C ILE A1209 " pdb=" CB ILE A1209 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA ILE A1350 " pdb=" N ILE A1350 " pdb=" C ILE A1350 " pdb=" CB ILE A1350 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA LEU A1246 " pdb=" N LEU A1246 " pdb=" C LEU A1246 " pdb=" CB LEU A1246 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1738 not shown) Planarity restraints: 1838 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1196 " -0.267 9.50e-02 1.11e+02 1.20e-01 8.82e+00 pdb=" NE ARG A1196 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A1196 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A1196 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A1196 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1472 " 0.252 9.50e-02 1.11e+02 1.13e-01 7.83e+00 pdb=" NE ARG A1472 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A1472 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A1472 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A1472 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 593 " -0.232 9.50e-02 1.11e+02 1.04e-01 6.62e+00 pdb=" NE ARG A 593 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 593 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 593 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 593 " -0.008 2.00e-02 2.50e+03 ... (remaining 1835 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 22 2.39 - 3.02: 6629 3.02 - 3.64: 16964 3.64 - 4.27: 25302 4.27 - 4.90: 43295 Nonbonded interactions: 92212 Sorted by model distance: nonbonded pdb=" OE1 GLN A1374 " pdb="MG MG A1604 " model vdw 1.760 2.170 nonbonded pdb=" O1B ATP A1603 " pdb="MG MG A1604 " model vdw 1.789 2.170 nonbonded pdb=" OG SER A 685 " pdb="MG MG A1602 " model vdw 2.077 2.170 nonbonded pdb=" OE1 GLN A 713 " pdb="MG MG A1602 " model vdw 2.160 2.170 nonbonded pdb=" OG SER A1333 " pdb="MG MG A1604 " model vdw 2.180 2.170 ... (remaining 92207 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.910 Find NCS groups from input model: 0.160 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 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 : 0.006 0.053 11022 Z= 0.417 Angle : 0.814 12.210 14972 Z= 0.586 Chirality : 0.057 0.272 1741 Planarity : 0.007 0.120 1838 Dihedral : 16.169 89.710 4018 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.25 % Allowed : 18.02 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.23), residues: 1327 helix: 0.47 (0.18), residues: 874 sheet: -0.54 (0.97), residues: 29 loop : -1.07 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 858 TYR 0.016 0.001 TYR A1297 PHE 0.024 0.002 PHE A 175 TRP 0.031 0.002 TRP A1245 HIS 0.006 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00599 (11022) covalent geometry : angle 0.81407 (14972) hydrogen bonds : bond 0.16693 ( 705) hydrogen bonds : angle 7.02900 ( 2070) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 158 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 227 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7610 (ttm) REVERT: A 243 SER cc_start: 0.8692 (m) cc_final: 0.8432 (p) REVERT: A 382 HIS cc_start: 0.7943 (m170) cc_final: 0.7536 (m-70) REVERT: A 416 LYS cc_start: 0.8248 (mtmt) cc_final: 0.7918 (mmtt) REVERT: A 443 MET cc_start: 0.7204 (mmm) cc_final: 0.6939 (mtt) REVERT: A 804 LYS cc_start: 0.8190 (tttt) cc_final: 0.7753 (ttpt) outliers start: 3 outliers final: 1 residues processed: 160 average time/residue: 0.1175 time to fit residues: 26.5012 Evaluate side-chains 134 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 317 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 ASN A 597 ASN ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1207 ASN A1363 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.156033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116708 restraints weight = 13797.224| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.95 r_work: 0.3300 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11022 Z= 0.162 Angle : 0.549 6.604 14972 Z= 0.288 Chirality : 0.041 0.173 1741 Planarity : 0.004 0.045 1838 Dihedral : 7.712 78.692 1520 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.28 % Allowed : 18.44 % Favored : 79.27 % 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: 1.12 (0.23), residues: 1327 helix: 1.61 (0.17), residues: 876 sheet: -1.15 (0.79), residues: 38 loop : -0.92 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1201 TYR 0.033 0.002 TYR A1032 PHE 0.014 0.001 PHE A 558 TRP 0.014 0.001 TRP A 142 HIS 0.006 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00372 (11022) covalent geometry : angle 0.54923 (14972) hydrogen bonds : bond 0.04407 ( 705) hydrogen bonds : angle 4.58936 ( 2070) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 54 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6956 (m-80) REVERT: A 186 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6950 (tt) REVERT: A 228 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8006 (mmt) REVERT: A 243 SER cc_start: 0.8944 (m) cc_final: 0.8663 (p) REVERT: A 416 LYS cc_start: 0.8619 (mtmt) cc_final: 0.8414 (mmtt) REVERT: A 505 MET cc_start: 0.8667 (mmm) cc_final: 0.8220 (mmm) REVERT: A 603 ILE cc_start: 0.8858 (mm) cc_final: 0.8634 (mt) REVERT: A 670 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8290 (mt-10) REVERT: A 804 LYS cc_start: 0.8735 (tttt) cc_final: 0.8337 (ttpt) REVERT: A 1106 ILE cc_start: 0.8208 (mm) cc_final: 0.8004 (mt) REVERT: A 1396 GLU cc_start: 0.8271 (tp30) cc_final: 0.8010 (tm-30) outliers start: 27 outliers final: 11 residues processed: 159 average time/residue: 0.1004 time to fit residues: 22.7424 Evaluate side-chains 135 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1085 MET Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1212 PHE Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1480 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 110 optimal weight: 0.4980 chunk 113 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 ASN ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.155784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.116917 restraints weight = 13757.811| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.93 r_work: 0.3302 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11022 Z= 0.129 Angle : 0.503 6.165 14972 Z= 0.262 Chirality : 0.039 0.160 1741 Planarity : 0.004 0.045 1838 Dihedral : 7.183 77.041 1515 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.54 % Allowed : 18.95 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.23), residues: 1327 helix: 1.86 (0.17), residues: 878 sheet: -1.12 (0.76), residues: 44 loop : -0.79 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 867 TYR 0.025 0.001 TYR A1032 PHE 0.013 0.001 PHE A 565 TRP 0.014 0.001 TRP A1507 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00287 (11022) covalent geometry : angle 0.50284 (14972) hydrogen bonds : bond 0.03918 ( 705) hydrogen bonds : angle 4.19152 ( 2070) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 54 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6999 (m-80) REVERT: A 186 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6882 (tt) REVERT: A 234 GLN cc_start: 0.7819 (pm20) cc_final: 0.7618 (pp30) REVERT: A 243 SER cc_start: 0.8937 (m) cc_final: 0.8624 (p) REVERT: A 416 LYS cc_start: 0.8637 (mtmt) cc_final: 0.8362 (mmtt) REVERT: A 441 ILE cc_start: 0.8545 (tt) cc_final: 0.8326 (tt) REVERT: A 505 MET cc_start: 0.8668 (mmm) cc_final: 0.8217 (mmm) REVERT: A 603 ILE cc_start: 0.8850 (mm) cc_final: 0.8630 (mt) REVERT: A 804 LYS cc_start: 0.8713 (tttt) cc_final: 0.8315 (ttpt) REVERT: A 997 LEU cc_start: 0.8193 (mp) cc_final: 0.7948 (mp) REVERT: A 1396 GLU cc_start: 0.8136 (tp30) cc_final: 0.7886 (tm-30) outliers start: 30 outliers final: 21 residues processed: 151 average time/residue: 0.0815 time to fit residues: 18.1525 Evaluate side-chains 148 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1085 MET Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1212 PHE Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1302 ARG Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1456 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 109 optimal weight: 0.0970 chunk 38 optimal weight: 0.2980 chunk 46 optimal weight: 0.6980 chunk 62 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 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 = 0.3912 r_free = 0.3912 target = 0.157388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118218 restraints weight = 13826.485| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.96 r_work: 0.3312 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11022 Z= 0.110 Angle : 0.477 6.073 14972 Z= 0.248 Chirality : 0.038 0.163 1741 Planarity : 0.003 0.045 1838 Dihedral : 6.972 74.826 1515 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.79 % Allowed : 19.63 % Favored : 77.58 % 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: 1.67 (0.23), residues: 1327 helix: 2.08 (0.17), residues: 875 sheet: -0.71 (0.68), residues: 54 loop : -0.84 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 867 TYR 0.024 0.001 TYR A1032 PHE 0.011 0.001 PHE A 175 TRP 0.015 0.001 TRP A1507 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00238 (11022) covalent geometry : angle 0.47670 (14972) hydrogen bonds : bond 0.03605 ( 705) hydrogen bonds : angle 3.96962 ( 2070) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.461 Fit side-chains REVERT: A 54 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.6859 (m-80) REVERT: A 142 TRP cc_start: 0.8088 (m100) cc_final: 0.7745 (m100) REVERT: A 186 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6800 (tt) REVERT: A 243 SER cc_start: 0.8904 (m) cc_final: 0.8606 (p) REVERT: A 327 MET cc_start: 0.7765 (ttt) cc_final: 0.7109 (mpp) REVERT: A 416 LYS cc_start: 0.8537 (mtmt) cc_final: 0.8305 (mmtt) REVERT: A 670 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8264 (mt-10) REVERT: A 696 ASP cc_start: 0.8188 (t0) cc_final: 0.7462 (m-30) REVERT: A 789 TYR cc_start: 0.8678 (m-80) cc_final: 0.8106 (m-80) REVERT: A 804 LYS cc_start: 0.8703 (tttt) cc_final: 0.8283 (ttpt) REVERT: A 997 LEU cc_start: 0.8342 (mp) cc_final: 0.8129 (mp) REVERT: A 1212 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.6779 (m-80) REVERT: A 1328 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8788 (t) REVERT: A 1396 GLU cc_start: 0.8187 (tp30) cc_final: 0.7926 (tm-30) outliers start: 33 outliers final: 21 residues processed: 157 average time/residue: 0.1091 time to fit residues: 24.8861 Evaluate side-chains 150 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1085 MET Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1212 PHE Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1328 THR Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1480 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN A 767 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.153101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.114048 restraints weight = 13812.641| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.94 r_work: 0.3261 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11022 Z= 0.167 Angle : 0.521 6.321 14972 Z= 0.269 Chirality : 0.041 0.173 1741 Planarity : 0.004 0.045 1838 Dihedral : 6.967 78.352 1515 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.96 % Allowed : 20.56 % Favored : 76.48 % 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: 1.58 (0.23), residues: 1327 helix: 2.01 (0.17), residues: 876 sheet: -0.74 (0.83), residues: 34 loop : -0.89 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1441 TYR 0.024 0.002 TYR A 318 PHE 0.012 0.001 PHE A 524 TRP 0.018 0.001 TRP A1507 HIS 0.006 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00395 (11022) covalent geometry : angle 0.52140 (14972) hydrogen bonds : bond 0.03847 ( 705) hydrogen bonds : angle 4.08252 ( 2070) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 54 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.6933 (m-80) REVERT: A 228 MET cc_start: 0.8458 (mmt) cc_final: 0.8246 (mmm) REVERT: A 327 MET cc_start: 0.7879 (ttt) cc_final: 0.7186 (mpp) REVERT: A 416 LYS cc_start: 0.8558 (mtmt) cc_final: 0.8331 (mmtt) REVERT: A 505 MET cc_start: 0.8712 (mmm) cc_final: 0.8279 (mmm) REVERT: A 696 ASP cc_start: 0.8240 (t0) cc_final: 0.7500 (m-30) REVERT: A 789 TYR cc_start: 0.8825 (m-80) cc_final: 0.8220 (m-80) REVERT: A 804 LYS cc_start: 0.8725 (tttt) cc_final: 0.8294 (ttpt) REVERT: A 997 LEU cc_start: 0.8349 (mp) cc_final: 0.8114 (mp) REVERT: A 1212 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.7086 (m-80) REVERT: A 1396 GLU cc_start: 0.8213 (tp30) cc_final: 0.7920 (tm-30) outliers start: 35 outliers final: 26 residues processed: 151 average time/residue: 0.1023 time to fit residues: 22.4232 Evaluate side-chains 151 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1085 MET Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1212 PHE Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1302 ARG Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1480 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 118 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 123 optimal weight: 0.0770 chunk 89 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.153828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114913 restraints weight = 13854.025| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.96 r_work: 0.3274 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11022 Z= 0.137 Angle : 0.496 6.012 14972 Z= 0.258 Chirality : 0.040 0.178 1741 Planarity : 0.003 0.045 1838 Dihedral : 6.957 80.518 1515 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.96 % Allowed : 20.81 % Favored : 76.23 % 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: 1.68 (0.23), residues: 1327 helix: 2.08 (0.17), residues: 878 sheet: -0.83 (0.67), residues: 54 loop : -0.81 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 867 TYR 0.021 0.001 TYR A1032 PHE 0.021 0.001 PHE A 329 TRP 0.016 0.001 TRP A1507 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00317 (11022) covalent geometry : angle 0.49621 (14972) hydrogen bonds : bond 0.03684 ( 705) hydrogen bonds : angle 4.00708 ( 2070) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 18 TRP cc_start: 0.6038 (m-90) cc_final: 0.5493 (m-10) REVERT: A 54 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.6976 (m-80) REVERT: A 186 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6847 (tt) REVERT: A 228 MET cc_start: 0.8464 (mmt) cc_final: 0.8246 (mmm) REVERT: A 327 MET cc_start: 0.7874 (ttt) cc_final: 0.7206 (mpp) REVERT: A 416 LYS cc_start: 0.8530 (mtmt) cc_final: 0.8325 (mmtt) REVERT: A 441 ILE cc_start: 0.8385 (tt) cc_final: 0.8164 (tt) REVERT: A 670 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8284 (mt-10) REVERT: A 696 ASP cc_start: 0.8269 (t0) cc_final: 0.7536 (m-30) REVERT: A 789 TYR cc_start: 0.8788 (m-80) cc_final: 0.8231 (m-80) REVERT: A 804 LYS cc_start: 0.8695 (tttt) cc_final: 0.8248 (ttpt) REVERT: A 997 LEU cc_start: 0.8312 (mp) cc_final: 0.8084 (mp) REVERT: A 1212 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.7169 (m-80) REVERT: A 1396 GLU cc_start: 0.8173 (tp30) cc_final: 0.7898 (tm-30) outliers start: 35 outliers final: 26 residues processed: 152 average time/residue: 0.1009 time to fit residues: 22.3722 Evaluate side-chains 150 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1085 MET Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1212 PHE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1480 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 83 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 772 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.153037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.114335 restraints weight = 13763.189| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.93 r_work: 0.3263 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11022 Z= 0.146 Angle : 0.502 6.075 14972 Z= 0.260 Chirality : 0.040 0.181 1741 Planarity : 0.003 0.045 1838 Dihedral : 6.966 80.979 1515 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.30 % Allowed : 20.73 % Favored : 75.97 % 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: 1.71 (0.23), residues: 1327 helix: 2.10 (0.17), residues: 878 sheet: -0.26 (0.76), residues: 44 loop : -0.90 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1441 TYR 0.022 0.001 TYR A1032 PHE 0.015 0.001 PHE A 329 TRP 0.017 0.001 TRP A1507 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00342 (11022) covalent geometry : angle 0.50159 (14972) hydrogen bonds : bond 0.03691 ( 705) hydrogen bonds : angle 4.00964 ( 2070) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 18 TRP cc_start: 0.6116 (m-90) cc_final: 0.5595 (m-10) REVERT: A 54 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.6987 (m-80) REVERT: A 228 MET cc_start: 0.8490 (mmt) cc_final: 0.8289 (mmm) REVERT: A 315 LYS cc_start: 0.8124 (tppt) cc_final: 0.7864 (tppp) REVERT: A 327 MET cc_start: 0.7878 (ttt) cc_final: 0.7209 (mpp) REVERT: A 416 LYS cc_start: 0.8555 (mtmt) cc_final: 0.8300 (mmtt) REVERT: A 441 ILE cc_start: 0.8368 (tt) cc_final: 0.8152 (tt) REVERT: A 505 MET cc_start: 0.8721 (mmm) cc_final: 0.8300 (mmm) REVERT: A 578 ASP cc_start: 0.7009 (t70) cc_final: 0.6763 (t0) REVERT: A 696 ASP cc_start: 0.8503 (t0) cc_final: 0.7660 (m-30) REVERT: A 717 ILE cc_start: 0.9310 (mm) cc_final: 0.8986 (mm) REVERT: A 804 LYS cc_start: 0.8697 (tttt) cc_final: 0.8246 (ttpt) REVERT: A 997 LEU cc_start: 0.8321 (mp) cc_final: 0.8086 (mp) REVERT: A 1396 GLU cc_start: 0.8171 (tp30) cc_final: 0.7900 (tm-30) outliers start: 39 outliers final: 28 residues processed: 155 average time/residue: 0.1037 time to fit residues: 23.2491 Evaluate side-chains 150 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1085 MET Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1302 ARG Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1314 VAL Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1480 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 82 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 123 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 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 = 0.3830 r_free = 0.3830 target = 0.150596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.111548 restraints weight = 13602.165| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.07 r_work: 0.3215 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11022 Z= 0.149 Angle : 0.519 9.943 14972 Z= 0.265 Chirality : 0.040 0.189 1741 Planarity : 0.003 0.044 1838 Dihedral : 6.930 82.068 1515 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.54 % Allowed : 21.32 % Favored : 76.14 % 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: 1.73 (0.23), residues: 1327 helix: 2.11 (0.17), residues: 878 sheet: -0.28 (0.75), residues: 44 loop : -0.88 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1441 TYR 0.022 0.001 TYR A1032 PHE 0.014 0.001 PHE A 329 TRP 0.015 0.001 TRP A1507 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00349 (11022) covalent geometry : angle 0.51918 (14972) hydrogen bonds : bond 0.03693 ( 705) hydrogen bonds : angle 4.00307 ( 2070) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 18 TRP cc_start: 0.6245 (m-90) cc_final: 0.5731 (m-10) REVERT: A 54 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7057 (m-80) REVERT: A 228 MET cc_start: 0.8499 (mmt) cc_final: 0.8298 (mmm) REVERT: A 315 LYS cc_start: 0.8003 (tppt) cc_final: 0.7761 (tppp) REVERT: A 327 MET cc_start: 0.7882 (ttt) cc_final: 0.7159 (mpp) REVERT: A 416 LYS cc_start: 0.8532 (mtmt) cc_final: 0.8215 (mmtt) REVERT: A 441 ILE cc_start: 0.8334 (tt) cc_final: 0.8109 (tt) REVERT: A 578 ASP cc_start: 0.6930 (t70) cc_final: 0.6686 (t0) REVERT: A 696 ASP cc_start: 0.8354 (t0) cc_final: 0.7557 (m-30) REVERT: A 717 ILE cc_start: 0.9270 (mm) cc_final: 0.8940 (mm) REVERT: A 804 LYS cc_start: 0.8653 (tttt) cc_final: 0.8182 (ttpt) REVERT: A 997 LEU cc_start: 0.8311 (mp) cc_final: 0.8063 (mp) REVERT: A 1396 GLU cc_start: 0.8073 (tp30) cc_final: 0.7799 (tm-30) outliers start: 30 outliers final: 24 residues processed: 149 average time/residue: 0.1015 time to fit residues: 21.9179 Evaluate side-chains 149 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1085 MET Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1480 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 81 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 47 optimal weight: 0.0470 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.148517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.109271 restraints weight = 13809.595| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.00 r_work: 0.3197 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11022 Z= 0.236 Angle : 0.587 7.676 14972 Z= 0.302 Chirality : 0.043 0.214 1741 Planarity : 0.004 0.041 1838 Dihedral : 7.150 87.384 1515 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.45 % Allowed : 21.74 % Favored : 75.80 % 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: 1.39 (0.23), residues: 1327 helix: 1.82 (0.17), residues: 884 sheet: -0.91 (0.86), residues: 34 loop : -0.91 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1441 TYR 0.024 0.002 TYR A1297 PHE 0.014 0.002 PHE A 524 TRP 0.019 0.001 TRP A1507 HIS 0.008 0.002 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00572 (11022) covalent geometry : angle 0.58686 (14972) hydrogen bonds : bond 0.04120 ( 705) hydrogen bonds : angle 4.24000 ( 2070) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.399 Fit side-chains REVERT: A 18 TRP cc_start: 0.6373 (m-90) cc_final: 0.5867 (m-10) REVERT: A 54 PHE cc_start: 0.7694 (OUTLIER) cc_final: 0.7042 (m-80) REVERT: A 315 LYS cc_start: 0.8115 (tppt) cc_final: 0.7873 (tppp) REVERT: A 327 MET cc_start: 0.8039 (ttt) cc_final: 0.7346 (mpp) REVERT: A 416 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8271 (mmtt) REVERT: A 441 ILE cc_start: 0.8417 (tt) cc_final: 0.8201 (tt) REVERT: A 505 MET cc_start: 0.8755 (mmm) cc_final: 0.8363 (mmm) REVERT: A 696 ASP cc_start: 0.8420 (t0) cc_final: 0.7634 (m-30) REVERT: A 717 ILE cc_start: 0.9350 (mm) cc_final: 0.9027 (mm) REVERT: A 804 LYS cc_start: 0.8740 (tttt) cc_final: 0.8331 (ttpt) REVERT: A 1396 GLU cc_start: 0.8269 (tp30) cc_final: 0.7978 (tm-30) outliers start: 29 outliers final: 26 residues processed: 145 average time/residue: 0.1068 time to fit residues: 22.3691 Evaluate side-chains 145 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1085 MET Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1314 VAL Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1480 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 3 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 126 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.0970 chunk 56 optimal weight: 0.1980 chunk 62 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** 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 = 0.3829 r_free = 0.3829 target = 0.150322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.113251 restraints weight = 13424.105| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.93 r_work: 0.3245 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11022 Z= 0.121 Angle : 0.504 8.433 14972 Z= 0.260 Chirality : 0.039 0.187 1741 Planarity : 0.003 0.043 1838 Dihedral : 6.908 83.185 1515 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.03 % Allowed : 22.34 % Favored : 75.63 % 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 (0.23), residues: 1327 helix: 2.07 (0.17), residues: 884 sheet: -0.97 (0.67), residues: 54 loop : -0.79 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1434 TYR 0.022 0.001 TYR A1297 PHE 0.014 0.001 PHE A 329 TRP 0.015 0.001 TRP A1507 HIS 0.006 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00272 (11022) covalent geometry : angle 0.50389 (14972) hydrogen bonds : bond 0.03651 ( 705) hydrogen bonds : angle 4.00638 ( 2070) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.490 Fit side-chains REVERT: A 18 TRP cc_start: 0.6327 (m-90) cc_final: 0.5871 (m-10) REVERT: A 54 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.7005 (m-80) REVERT: A 315 LYS cc_start: 0.8005 (tppt) cc_final: 0.7757 (tppp) REVERT: A 327 MET cc_start: 0.7876 (ttt) cc_final: 0.7152 (mpp) REVERT: A 416 LYS cc_start: 0.8504 (mtmt) cc_final: 0.8242 (mmtt) REVERT: A 441 ILE cc_start: 0.8270 (tt) cc_final: 0.8031 (tt) REVERT: A 505 MET cc_start: 0.8629 (mmm) cc_final: 0.8189 (mmm) REVERT: A 696 ASP cc_start: 0.8215 (t0) cc_final: 0.7407 (m-30) REVERT: A 717 ILE cc_start: 0.9248 (mm) cc_final: 0.8959 (mm) REVERT: A 804 LYS cc_start: 0.8613 (tttt) cc_final: 0.8175 (ttpt) REVERT: A 1396 GLU cc_start: 0.8048 (tp30) cc_final: 0.7782 (tm-30) outliers start: 24 outliers final: 23 residues processed: 144 average time/residue: 0.1077 time to fit residues: 22.4433 Evaluate side-chains 144 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1085 MET Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1401 SER Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1480 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 76 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 132 optimal weight: 0.2980 chunk 19 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.150001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.112901 restraints weight = 13564.487| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.93 r_work: 0.3213 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11022 Z= 0.131 Angle : 0.505 7.663 14972 Z= 0.260 Chirality : 0.039 0.199 1741 Planarity : 0.003 0.043 1838 Dihedral : 6.787 80.237 1515 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.37 % Allowed : 21.83 % Favored : 75.80 % 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: 1.76 (0.23), residues: 1327 helix: 2.12 (0.17), residues: 884 sheet: -0.96 (0.67), residues: 54 loop : -0.76 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1165 TYR 0.023 0.001 TYR A1032 PHE 0.013 0.001 PHE A 329 TRP 0.017 0.001 TRP A1507 HIS 0.005 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00302 (11022) covalent geometry : angle 0.50518 (14972) hydrogen bonds : bond 0.03595 ( 705) hydrogen bonds : angle 3.96098 ( 2070) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2781.92 seconds wall clock time: 48 minutes 25.59 seconds (2905.59 seconds total)