Starting phenix.real_space_refine on Tue May 5 00:35:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pe5_71554/05_2026/9pe5_71554_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pe5_71554/05_2026/9pe5_71554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pe5_71554/05_2026/9pe5_71554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pe5_71554/05_2026/9pe5_71554.map" model { file = "/net/cci-nas-00/data/ceres_data/9pe5_71554/05_2026/9pe5_71554_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pe5_71554/05_2026/9pe5_71554_trim.cif" } resolution = 2.8 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= 0.035 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 1 5.49 5 S 67 5.16 5 C 8061 2.51 5 N 2003 2.21 5 O 2116 1.98 5 H 11406 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23654 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 23252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1502, 23252 Classifications: {'peptide': 1502} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 64, 'TRANS': 1436} Chain breaks: 15 Unresolved non-hydrogen bonds: 442 Unresolved non-hydrogen angles: 547 Unresolved non-hydrogen dihedrals: 370 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ASN:plan1': 4, 'ARG:plan': 14, 'ASP:plan': 13, 'GLU:plan': 12, 'TYR:plan': 7, 'GLN:plan1': 4, 'PHE:plan': 3, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 267 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 363 Unusual residues: {'3PE': 1, 'LMN': 1, 'Y01': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 4.44, per 1000 atoms: 0.19 Number of scatterers: 23654 At special positions: 0 Unit cell: (90.143, 112.472, 137.282, 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 67 16.00 P 1 15.00 O 2116 8.00 N 2003 7.00 C 8061 6.00 H 11406 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A1328 " - pdb=" SG CYS A1345 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A1849 " Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 772.8 milliseconds 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2854 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 3 sheets defined 69.7% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 137 through 143 Processing helix chain 'A' and resid 148 through 154 removed outlier: 3.692A pdb=" N ASP A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 178 through 198 Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.591A pdb=" N LYS A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 269 through 277 Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.503A pdb=" N GLN A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 296 " --> pdb=" O LYS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 314 removed outlier: 3.667A pdb=" N GLU A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 Processing helix chain 'A' and resid 321 through 338 Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.547A pdb=" N GLN A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 357 Processing helix chain 'A' and resid 357 through 369 removed outlier: 4.261A pdb=" N ILE A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 369 " --> pdb=" O ILE A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 389 through 397 removed outlier: 3.713A pdb=" N LEU A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 422 through 429 removed outlier: 4.475A pdb=" N GLY A 427 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 429 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 443 through 452 removed outlier: 3.554A pdb=" N HIS A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 470 removed outlier: 3.510A pdb=" N TRP A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 488 through 515 removed outlier: 4.328A pdb=" N GLY A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 553 removed outlier: 3.828A pdb=" N ARG A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 561 through 583 Processing helix chain 'A' and resid 590 through 594 removed outlier: 3.849A pdb=" N LYS A 594 " --> pdb=" O SER A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 640 removed outlier: 3.985A pdb=" N TRP A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 637 " --> pdb=" O TYR A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 654 removed outlier: 4.772A pdb=" N ASP A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) Proline residue: A 647 - end of helix Processing helix chain 'A' and resid 671 through 710 removed outlier: 3.636A pdb=" N PHE A 689 " --> pdb=" O PHE A 685 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 692 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR A 693 " --> pdb=" O PHE A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 734 Proline residue: A 727 - end of helix Processing helix chain 'A' and resid 745 through 764 removed outlier: 3.942A pdb=" N LEU A 749 " --> pdb=" O LYS A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 773 removed outlier: 3.535A pdb=" N GLN A 773 " --> pdb=" O ILE A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 798 removed outlier: 3.500A pdb=" N VAL A 797 " --> pdb=" O PRO A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 826 removed outlier: 3.545A pdb=" N LEU A 826 " --> pdb=" O PHE A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 839 Processing helix chain 'A' and resid 856 through 861 Processing helix chain 'A' and resid 871 through 880 Processing helix chain 'A' and resid 880 through 893 Processing helix chain 'A' and resid 935 through 947 Processing helix chain 'A' and resid 949 through 971 removed outlier: 4.035A pdb=" N THR A 953 " --> pdb=" O THR A 949 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 960 " --> pdb=" O GLY A 956 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER A 961 " --> pdb=" O PHE A 957 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 962 " --> pdb=" O MET A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 980 removed outlier: 3.585A pdb=" N VAL A 976 " --> pdb=" O ASN A 972 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 997 Processing helix chain 'A' and resid 1006 through 1010 removed outlier: 3.577A pdb=" N PHE A1010 " --> pdb=" O LEU A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1025 Processing helix chain 'A' and resid 1082 through 1091 removed outlier: 4.364A pdb=" N ILE A1091 " --> pdb=" O ASN A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1113 Processing helix chain 'A' and resid 1114 through 1121 Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1201 through 1206 Processing helix chain 'A' and resid 1220 through 1233 removed outlier: 3.733A pdb=" N ALA A1225 " --> pdb=" O GLU A1221 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY A1226 " --> pdb=" O ASP A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1271 Processing helix chain 'A' and resid 1272 through 1280 removed outlier: 3.582A pdb=" N TYR A1276 " --> pdb=" O SER A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1292 Processing helix chain 'A' and resid 1294 through 1324 removed outlier: 4.353A pdb=" N HIS A1298 " --> pdb=" O HIS A1294 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1382 removed outlier: 3.549A pdb=" N TRP A1354 " --> pdb=" O PRO A1350 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL A1355 " --> pdb=" O ALA A1351 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG A1356 " --> pdb=" O VAL A1352 " (cutoff:3.500A) Proline residue: A1372 - end of helix Processing helix chain 'A' and resid 1383 through 1394 Processing helix chain 'A' and resid 1411 through 1424 removed outlier: 3.502A pdb=" N ILE A1419 " --> pdb=" O SER A1415 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A1420 " --> pdb=" O ASP A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1447 removed outlier: 4.435A pdb=" N GLY A1447 " --> pdb=" O SER A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1451 through 1467 Processing helix chain 'A' and resid 1471 through 1489 removed outlier: 4.104A pdb=" N PHE A1475 " --> pdb=" O PRO A1471 " (cutoff:3.500A) Proline residue: A1486 - end of helix Processing helix chain 'A' and resid 1495 through 1512 Processing helix chain 'A' and resid 1521 through 1530 Processing helix chain 'A' and resid 1555 through 1583 removed outlier: 5.209A pdb=" N ILE A1566 " --> pdb=" O MET A1562 " (cutoff:3.500A) Proline residue: A1567 - end of helix Processing helix chain 'A' and resid 1598 through 1621 Proline residue: A1609 - end of helix Processing helix chain 'A' and resid 1640 through 1665 Processing helix chain 'A' and resid 1668 through 1695 Processing helix chain 'A' and resid 1726 through 1759 removed outlier: 3.502A pdb=" N GLN A1754 " --> pdb=" O ILE A1750 " (cutoff:3.500A) Proline residue: A1756 - end of helix Processing helix chain 'A' and resid 1762 through 1775 Processing helix chain 'A' and resid 1786 through 1825 Proline residue: A1818 - end of helix removed outlier: 4.028A pdb=" N ALA A1823 " --> pdb=" O ALA A1819 " (cutoff:3.500A) Processing helix chain 'A' and resid 1834 through 1838 removed outlier: 4.103A pdb=" N VAL A1837 " --> pdb=" O ASP A1834 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 373 Processing sheet with id=AA2, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AA3, first strand: chain 'A' and resid 1068 through 1071 removed outlier: 3.594A pdb=" N PHE A1068 " --> pdb=" O LEU A1051 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU A1033 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE A 842 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU A1001 " --> pdb=" O PHE A 842 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL A 844 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N SER A1003 " --> pdb=" O VAL A 844 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR A 846 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR A 843 " --> pdb=" O GLN A1099 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA A1149 " --> pdb=" O ASN A1200 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ARG A1235 " --> pdb=" O VAL A1148 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 2088 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: 5.80 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11383 1.03 - 1.23: 53 1.23 - 1.42: 5275 1.42 - 1.61: 7170 1.61 - 1.81: 109 Bond restraints: 23990 Sorted by residual: bond pdb=" CAY Y01 A2001 " pdb=" OAW Y01 A2001 " ideal model delta sigma weight residual 1.332 1.433 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" CAY Y01 A2009 " pdb=" OAW Y01 A2009 " ideal model delta sigma weight residual 1.332 1.433 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" CAY Y01 A2004 " pdb=" OAW Y01 A2004 " ideal model delta sigma weight residual 1.332 1.431 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" CAY Y01 A2006 " pdb=" OAW Y01 A2006 " ideal model delta sigma weight residual 1.332 1.430 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" CAY Y01 A2003 " pdb=" OAW Y01 A2003 " ideal model delta sigma weight residual 1.332 1.429 -0.097 2.00e-02 2.50e+03 2.33e+01 ... (remaining 23985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.92: 42921 5.92 - 11.84: 40 11.84 - 17.76: 6 17.76 - 23.68: 2 23.68 - 29.60: 4 Bond angle restraints: 42973 Sorted by residual: angle pdb=" SD MET A1770 " pdb=" CE MET A1770 " pdb=" HE3 MET A1770 " ideal model delta sigma weight residual 109.00 79.40 29.60 3.00e+00 1.11e-01 9.74e+01 angle pdb=" SD MET A1770 " pdb=" CE MET A1770 " pdb=" HE2 MET A1770 " ideal model delta sigma weight residual 109.00 79.79 29.21 3.00e+00 1.11e-01 9.48e+01 angle pdb=" HE1 MET A1770 " pdb=" CE MET A1770 " pdb=" HE3 MET A1770 " ideal model delta sigma weight residual 110.00 81.06 28.94 3.00e+00 1.11e-01 9.30e+01 angle pdb=" HE1 MET A1770 " pdb=" CE MET A1770 " pdb=" HE2 MET A1770 " ideal model delta sigma weight residual 110.00 81.10 28.90 3.00e+00 1.11e-01 9.28e+01 angle pdb=" HE2 MET A1770 " pdb=" CE MET A1770 " pdb=" HE3 MET A1770 " ideal model delta sigma weight residual 110.00 132.53 -22.53 3.00e+00 1.11e-01 5.64e+01 ... (remaining 42968 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.40: 11434 27.40 - 54.80: 380 54.80 - 82.20: 75 82.20 - 109.61: 23 109.61 - 137.01: 21 Dihedral angle restraints: 11933 sinusoidal: 6489 harmonic: 5444 Sorted by residual: dihedral pdb=" CA ASP A1197 " pdb=" C ASP A1197 " pdb=" N PHE A1198 " pdb=" CA PHE A1198 " ideal model delta harmonic sigma weight residual 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CBD LMN A2007 " pdb=" CBF LMN A2007 " pdb=" CBH LMN A2007 " pdb=" CBJ LMN A2007 " ideal model delta sinusoidal sigma weight residual 180.82 43.81 137.01 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" CBG LMN A2007 " pdb=" CBI LMN A2007 " pdb=" CBK LMN A2007 " pdb=" CBQ LMN A2007 " ideal model delta sinusoidal sigma weight residual 181.33 59.52 121.81 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 11930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 1906 0.151 - 0.301: 17 0.301 - 0.452: 20 0.452 - 0.602: 0 0.602 - 0.752: 1 Chirality restraints: 1944 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.38e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A1849 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" C1 BMA B 3 " pdb=" O4 NAG B 2 " pdb=" C2 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 8.33e+00 ... (remaining 1941 not shown) Planarity restraints: 3504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.078 2.00e-02 2.50e+03 6.53e-02 5.33e+01 pdb=" C7 NAG B 2 " -0.016 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.057 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.107 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.053 2.00e-02 2.50e+03 4.40e-02 2.42e+01 pdb=" C7 NAG B 1 " -0.018 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.041 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.069 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1852 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C GLY A1852 " 0.031 2.00e-02 2.50e+03 pdb=" O GLY A1852 " -0.011 2.00e-02 2.50e+03 pdb=" N SER A1853 " -0.010 2.00e-02 2.50e+03 ... (remaining 3501 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1333 2.21 - 2.81: 48506 2.81 - 3.41: 65353 3.41 - 4.00: 86086 4.00 - 4.60: 134038 Nonbonded interactions: 335316 Sorted by model distance: nonbonded pdb=" HG SER A 195 " pdb=" OE2 GLU A1096 " model vdw 1.614 2.450 nonbonded pdb=" OE1 GLU A 851 " pdb=" H GLU A 851 " model vdw 1.683 2.450 nonbonded pdb=" O THR A 218 " pdb="HH22 ARG A1207 " model vdw 1.687 2.450 nonbonded pdb=" OD1 ASP A1053 " pdb=" H GLY A1054 " model vdw 1.691 2.450 nonbonded pdb=" O LEU A 354 " pdb=" HG1 THR A 359 " model vdw 1.709 2.450 ... (remaining 335311 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.490 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 0.101 12589 Z= 0.263 Angle : 0.803 12.971 17150 Z= 0.359 Chirality : 0.060 0.752 1944 Planarity : 0.004 0.065 2098 Dihedral : 16.624 137.007 4984 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.25 % Allowed : 4.56 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 (0.22), residues: 1470 helix: 1.73 (0.17), residues: 942 sheet: -0.09 (0.73), residues: 54 loop : -0.52 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 649 TYR 0.013 0.001 TYR A 308 PHE 0.019 0.001 PHE A 517 TRP 0.015 0.001 TRP A 625 HIS 0.004 0.001 HIS A1013 Details of bonding type rmsd covalent geometry : bond 0.00538 (12584) covalent geometry : angle 0.79793 (17137) SS BOND : bond 0.00446 ( 2) SS BOND : angle 1.22447 ( 4) hydrogen bonds : bond 0.14314 ( 718) hydrogen bonds : angle 5.72704 ( 2088) link_BETA1-4 : bond 0.00839 ( 2) link_BETA1-4 : angle 3.43660 ( 6) link_NAG-ASN : bond 0.00387 ( 1) link_NAG-ASN : angle 4.86857 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue TYR 558 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue TYR 710 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue SER 714 is missing expected H atoms. Skipping. Residue ILE 742 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue VAL 797 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue TYR 935 is missing expected H atoms. Skipping. Residue TYR 1156 is missing expected H atoms. Skipping. Residue THR 1178 is missing expected H atoms. Skipping. Residue LEU 1179 is missing expected H atoms. Skipping. Residue LEU 1191 is missing expected H atoms. Skipping. Residue TYR 1193 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue LYS 1385 is missing expected H atoms. Skipping. Residue LEU 1414 is missing expected H atoms. Skipping. Residue SER 1415 is missing expected H atoms. Skipping. Residue LEU 1417 is missing expected H atoms. Skipping. Residue ILE 1419 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue VAL 1526 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue MET 1621 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue MET 1694 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue ILE 1769 is missing expected H atoms. Skipping. Residue LEU 1771 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue ILE 1780 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue LYS 1798 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 218 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 ARG cc_start: 0.8353 (mtt90) cc_final: 0.8149 (mmt-90) REVERT: A 745 LYS cc_start: 0.8593 (mttt) cc_final: 0.8287 (mppt) REVERT: A 760 SER cc_start: 0.8549 (t) cc_final: 0.8329 (p) REVERT: A 778 HIS cc_start: 0.6932 (m-70) cc_final: 0.6525 (m-70) REVERT: A 791 ARG cc_start: 0.7761 (ttp80) cc_final: 0.7506 (ttp80) REVERT: A 824 GLN cc_start: 0.7732 (tt0) cc_final: 0.7523 (tp-100) REVERT: A 872 LEU cc_start: 0.8709 (tp) cc_final: 0.8424 (tm) REVERT: A 874 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8354 (tp30) REVERT: A 878 GLN cc_start: 0.7729 (tt0) cc_final: 0.7107 (tm-30) REVERT: A 988 ARG cc_start: 0.7642 (mtm110) cc_final: 0.7416 (mmt180) REVERT: A 1082 LYS cc_start: 0.7858 (pttt) cc_final: 0.7556 (pttp) REVERT: A 1083 SER cc_start: 0.8939 (t) cc_final: 0.8656 (m) REVERT: A 1243 GLN cc_start: 0.7832 (tt0) cc_final: 0.7555 (tt0) REVERT: A 1491 PRO cc_start: 0.7790 (Cg_exo) cc_final: 0.7536 (Cg_endo) REVERT: A 1796 MET cc_start: 0.7633 (mmm) cc_final: 0.7083 (mtp) REVERT: A 1801 CYS cc_start: 0.8488 (t) cc_final: 0.7956 (t) outliers start: 3 outliers final: 1 residues processed: 221 average time/residue: 1.2314 time to fit residues: 296.9916 Evaluate side-chains 143 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1088 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 HIS A 982 ASN A1469 GLN A1493 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.134756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.097860 restraints weight = 50337.019| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.49 r_work: 0.3010 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12589 Z= 0.161 Angle : 0.558 8.892 17150 Z= 0.282 Chirality : 0.040 0.252 1944 Planarity : 0.004 0.041 2098 Dihedral : 13.451 131.466 2365 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.91 % Allowed : 9.54 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 1.48 (0.22), residues: 1470 helix: 1.78 (0.17), residues: 953 sheet: 0.21 (0.73), residues: 54 loop : -0.57 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 725 TYR 0.014 0.001 TYR A1800 PHE 0.016 0.001 PHE A 517 TRP 0.014 0.001 TRP A 625 HIS 0.004 0.001 HIS A1467 Details of bonding type rmsd covalent geometry : bond 0.00353 (12584) covalent geometry : angle 0.55537 (17137) SS BOND : bond 0.00396 ( 2) SS BOND : angle 0.46201 ( 4) hydrogen bonds : bond 0.05258 ( 718) hydrogen bonds : angle 4.58637 ( 2088) link_BETA1-4 : bond 0.00894 ( 2) link_BETA1-4 : angle 2.71032 ( 6) link_NAG-ASN : bond 0.00129 ( 1) link_NAG-ASN : angle 1.93171 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue TYR 558 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue TYR 710 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue SER 714 is missing expected H atoms. Skipping. Residue ILE 742 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue VAL 797 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue TYR 935 is missing expected H atoms. Skipping. Residue TYR 1156 is missing expected H atoms. Skipping. Residue THR 1178 is missing expected H atoms. Skipping. Residue LEU 1179 is missing expected H atoms. Skipping. Residue LEU 1191 is missing expected H atoms. Skipping. Residue TYR 1193 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue LYS 1385 is missing expected H atoms. Skipping. Residue LEU 1414 is missing expected H atoms. Skipping. Residue SER 1415 is missing expected H atoms. Skipping. Residue LEU 1417 is missing expected H atoms. Skipping. Residue ILE 1419 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue VAL 1526 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue MET 1621 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue MET 1694 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue ILE 1769 is missing expected H atoms. Skipping. Residue LEU 1771 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue ILE 1780 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue LYS 1798 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 745 LYS cc_start: 0.8601 (mttt) cc_final: 0.8261 (mppt) REVERT: A 771 HIS cc_start: 0.8144 (m-70) cc_final: 0.7538 (m90) REVERT: A 778 HIS cc_start: 0.6915 (m-70) cc_final: 0.6480 (m-70) REVERT: A 791 ARG cc_start: 0.7817 (ttp80) cc_final: 0.7515 (ttp80) REVERT: A 824 GLN cc_start: 0.7884 (tt0) cc_final: 0.7629 (tp-100) REVERT: A 872 LEU cc_start: 0.8520 (tp) cc_final: 0.8219 (tm) REVERT: A 874 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8464 (tp30) REVERT: A 878 GLN cc_start: 0.7623 (tt0) cc_final: 0.6985 (tm-30) REVERT: A 886 CYS cc_start: 0.7288 (m) cc_final: 0.7041 (t) REVERT: A 988 ARG cc_start: 0.7758 (mtm110) cc_final: 0.7441 (mmt180) REVERT: A 1082 LYS cc_start: 0.7664 (pttt) cc_final: 0.7436 (pttp) REVERT: A 1223 ILE cc_start: 0.7859 (mp) cc_final: 0.7535 (tp) REVERT: A 1228 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7981 (t0) REVERT: A 1243 GLN cc_start: 0.8003 (tt0) cc_final: 0.7680 (tt0) REVERT: A 1445 PHE cc_start: 0.7767 (m-80) cc_final: 0.7545 (m-80) REVERT: A 1491 PRO cc_start: 0.7661 (Cg_exo) cc_final: 0.7363 (Cg_endo) REVERT: A 1795 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7755 (mpp-170) REVERT: A 1796 MET cc_start: 0.7474 (mmm) cc_final: 0.6950 (mtp) REVERT: A 1801 CYS cc_start: 0.8442 (t) cc_final: 0.8078 (t) outliers start: 23 outliers final: 9 residues processed: 163 average time/residue: 1.0105 time to fit residues: 183.2063 Evaluate side-chains 146 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1228 ASN Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1746 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 127 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 128 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS A 563 HIS A 977 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.096857 restraints weight = 50201.128| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.49 r_work: 0.2993 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12589 Z= 0.172 Angle : 0.534 8.976 17150 Z= 0.269 Chirality : 0.039 0.236 1944 Planarity : 0.004 0.042 2098 Dihedral : 10.934 129.271 2365 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.91 % Allowed : 10.53 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 (0.22), residues: 1470 helix: 1.92 (0.17), residues: 949 sheet: 0.44 (0.72), residues: 54 loop : -0.47 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 382 TYR 0.019 0.001 TYR A1800 PHE 0.017 0.001 PHE A 517 TRP 0.014 0.001 TRP A 625 HIS 0.004 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00391 (12584) covalent geometry : angle 0.53059 (17137) SS BOND : bond 0.00411 ( 2) SS BOND : angle 0.40282 ( 4) hydrogen bonds : bond 0.04991 ( 718) hydrogen bonds : angle 4.36086 ( 2088) link_BETA1-4 : bond 0.00290 ( 2) link_BETA1-4 : angle 2.83180 ( 6) link_NAG-ASN : bond 0.00084 ( 1) link_NAG-ASN : angle 1.86960 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue TYR 558 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue TYR 710 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue SER 714 is missing expected H atoms. Skipping. Residue ILE 742 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue VAL 797 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue TYR 935 is missing expected H atoms. Skipping. Residue TYR 1156 is missing expected H atoms. Skipping. Residue THR 1178 is missing expected H atoms. Skipping. Residue LEU 1179 is missing expected H atoms. Skipping. Residue LEU 1191 is missing expected H atoms. Skipping. Residue TYR 1193 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue LYS 1385 is missing expected H atoms. Skipping. Residue LEU 1414 is missing expected H atoms. Skipping. Residue SER 1415 is missing expected H atoms. Skipping. Residue LEU 1417 is missing expected H atoms. Skipping. Residue ILE 1419 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue VAL 1526 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue MET 1621 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue MET 1694 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue ILE 1769 is missing expected H atoms. Skipping. Residue LEU 1771 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue ILE 1780 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue LYS 1798 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 HIS cc_start: 0.8144 (m-70) cc_final: 0.7561 (m90) REVERT: A 778 HIS cc_start: 0.6922 (m-70) cc_final: 0.6436 (m-70) REVERT: A 791 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7589 (ttp80) REVERT: A 824 GLN cc_start: 0.7882 (tt0) cc_final: 0.7637 (tp-100) REVERT: A 872 LEU cc_start: 0.8574 (tp) cc_final: 0.8286 (tm) REVERT: A 874 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8372 (tp30) REVERT: A 878 GLN cc_start: 0.7582 (tt0) cc_final: 0.6967 (tm-30) REVERT: A 977 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8427 (mp10) REVERT: A 988 ARG cc_start: 0.7731 (mtm110) cc_final: 0.7426 (mmt180) REVERT: A 1082 LYS cc_start: 0.7692 (pttt) cc_final: 0.7469 (pttp) REVERT: A 1223 ILE cc_start: 0.7809 (mp) cc_final: 0.7513 (tp) REVERT: A 1228 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7972 (t0) REVERT: A 1243 GLN cc_start: 0.8035 (tt0) cc_final: 0.7792 (pt0) REVERT: A 1491 PRO cc_start: 0.7666 (Cg_exo) cc_final: 0.7339 (Cg_endo) REVERT: A 1492 HIS cc_start: 0.8795 (m90) cc_final: 0.8571 (m90) REVERT: A 1498 ASP cc_start: 0.8653 (m-30) cc_final: 0.8198 (t0) REVERT: A 1618 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.6337 (m-80) REVERT: A 1795 ARG cc_start: 0.7970 (mtt180) cc_final: 0.7728 (mpp-170) REVERT: A 1796 MET cc_start: 0.7487 (mmm) cc_final: 0.6948 (mtp) REVERT: A 1801 CYS cc_start: 0.8290 (t) cc_final: 0.7831 (t) outliers start: 23 outliers final: 8 residues processed: 158 average time/residue: 0.9995 time to fit residues: 175.7625 Evaluate side-chains 145 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1228 ASN Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1618 PHE Chi-restraints excluded: chain A residue 1746 LEU Chi-restraints excluded: chain A residue 1759 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 132 optimal weight: 0.6980 chunk 55 optimal weight: 0.0970 chunk 145 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS A1754 GLN A1826 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.134527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.097491 restraints weight = 50104.121| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.50 r_work: 0.3000 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12589 Z= 0.143 Angle : 0.501 7.887 17150 Z= 0.254 Chirality : 0.039 0.354 1944 Planarity : 0.004 0.041 2098 Dihedral : 9.842 121.134 2365 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.49 % Allowed : 11.19 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 1.83 (0.22), residues: 1470 helix: 2.05 (0.17), residues: 949 sheet: 0.51 (0.71), residues: 54 loop : -0.43 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 376 TYR 0.017 0.001 TYR A1800 PHE 0.015 0.001 PHE A1499 TRP 0.013 0.001 TRP A 625 HIS 0.004 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00322 (12584) covalent geometry : angle 0.49839 (17137) SS BOND : bond 0.00346 ( 2) SS BOND : angle 0.36822 ( 4) hydrogen bonds : bond 0.04593 ( 718) hydrogen bonds : angle 4.20085 ( 2088) link_BETA1-4 : bond 0.00340 ( 2) link_BETA1-4 : angle 2.29432 ( 6) link_NAG-ASN : bond 0.00218 ( 1) link_NAG-ASN : angle 1.59494 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue TYR 558 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue TYR 710 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue SER 714 is missing expected H atoms. Skipping. Residue ILE 742 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue VAL 797 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue TYR 935 is missing expected H atoms. Skipping. Residue TYR 1156 is missing expected H atoms. Skipping. Residue THR 1178 is missing expected H atoms. Skipping. Residue LEU 1179 is missing expected H atoms. Skipping. Residue LEU 1191 is missing expected H atoms. Skipping. Residue TYR 1193 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue LYS 1385 is missing expected H atoms. Skipping. Residue LEU 1414 is missing expected H atoms. Skipping. Residue SER 1415 is missing expected H atoms. Skipping. Residue LEU 1417 is missing expected H atoms. Skipping. Residue ILE 1419 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue VAL 1526 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue MET 1621 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue MET 1694 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue ILE 1769 is missing expected H atoms. Skipping. Residue LEU 1771 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue ILE 1780 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue LYS 1798 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 HIS cc_start: 0.8133 (m-70) cc_final: 0.7585 (m90) REVERT: A 778 HIS cc_start: 0.6936 (m-70) cc_final: 0.6464 (m-70) REVERT: A 779 GLN cc_start: 0.7272 (pt0) cc_final: 0.6929 (mt0) REVERT: A 824 GLN cc_start: 0.7870 (tt0) cc_final: 0.7635 (tp-100) REVERT: A 872 LEU cc_start: 0.8573 (tp) cc_final: 0.8301 (tm) REVERT: A 878 GLN cc_start: 0.7582 (tt0) cc_final: 0.6960 (tm-30) REVERT: A 977 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8334 (mp10) REVERT: A 988 ARG cc_start: 0.7722 (mtm110) cc_final: 0.7418 (mmt180) REVERT: A 1082 LYS cc_start: 0.7675 (pttt) cc_final: 0.7448 (pttp) REVERT: A 1138 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.8006 (mtm180) REVERT: A 1223 ILE cc_start: 0.7771 (mp) cc_final: 0.7481 (tp) REVERT: A 1228 ASN cc_start: 0.8200 (OUTLIER) cc_final: 0.7957 (t0) REVERT: A 1243 GLN cc_start: 0.8098 (tt0) cc_final: 0.7837 (pt0) REVERT: A 1491 PRO cc_start: 0.7684 (Cg_exo) cc_final: 0.7376 (Cg_endo) REVERT: A 1492 HIS cc_start: 0.8782 (m90) cc_final: 0.8213 (m-70) REVERT: A 1494 PHE cc_start: 0.8842 (m-80) cc_final: 0.8617 (m-80) REVERT: A 1498 ASP cc_start: 0.8648 (m-30) cc_final: 0.8206 (t0) REVERT: A 1618 PHE cc_start: 0.6868 (OUTLIER) cc_final: 0.6395 (m-80) REVERT: A 1795 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7780 (mpp-170) REVERT: A 1796 MET cc_start: 0.7566 (mmm) cc_final: 0.6956 (mtp) REVERT: A 1801 CYS cc_start: 0.8334 (t) cc_final: 0.7868 (t) outliers start: 18 outliers final: 9 residues processed: 155 average time/residue: 1.0538 time to fit residues: 181.1108 Evaluate side-chains 148 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 886 CYS Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1228 ASN Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1618 PHE Chi-restraints excluded: chain A residue 1746 LEU Chi-restraints excluded: chain A residue 1759 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 85 optimal weight: 0.0050 chunk 145 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS A1754 GLN A1826 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.134395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.097448 restraints weight = 49872.280| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.49 r_work: 0.3004 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12589 Z= 0.135 Angle : 0.485 7.609 17150 Z= 0.247 Chirality : 0.037 0.217 1944 Planarity : 0.004 0.040 2098 Dihedral : 9.249 113.145 2365 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.33 % Allowed : 11.77 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 1.95 (0.22), residues: 1470 helix: 2.15 (0.17), residues: 946 sheet: 0.17 (0.65), residues: 64 loop : -0.34 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 376 TYR 0.019 0.001 TYR A1800 PHE 0.018 0.001 PHE A1499 TRP 0.013 0.001 TRP A 625 HIS 0.003 0.001 HIS A1294 Details of bonding type rmsd covalent geometry : bond 0.00304 (12584) covalent geometry : angle 0.48338 (17137) SS BOND : bond 0.00305 ( 2) SS BOND : angle 0.31941 ( 4) hydrogen bonds : bond 0.04446 ( 718) hydrogen bonds : angle 4.10464 ( 2088) link_BETA1-4 : bond 0.00260 ( 2) link_BETA1-4 : angle 2.05586 ( 6) link_NAG-ASN : bond 0.00234 ( 1) link_NAG-ASN : angle 1.59682 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue TYR 558 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue TYR 710 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue SER 714 is missing expected H atoms. Skipping. Residue ILE 742 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue VAL 797 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue TYR 935 is missing expected H atoms. Skipping. Residue TYR 1156 is missing expected H atoms. Skipping. Residue THR 1178 is missing expected H atoms. Skipping. Residue LEU 1179 is missing expected H atoms. Skipping. Residue LEU 1191 is missing expected H atoms. Skipping. Residue TYR 1193 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue LYS 1385 is missing expected H atoms. Skipping. Residue LEU 1414 is missing expected H atoms. Skipping. Residue SER 1415 is missing expected H atoms. Skipping. Residue LEU 1417 is missing expected H atoms. Skipping. Residue ILE 1419 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue VAL 1526 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue MET 1621 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue MET 1694 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue ILE 1769 is missing expected H atoms. Skipping. Residue LEU 1771 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue ILE 1780 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue LYS 1798 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 HIS cc_start: 0.8102 (m-70) cc_final: 0.7601 (m90) REVERT: A 778 HIS cc_start: 0.6961 (m-70) cc_final: 0.6562 (m-70) REVERT: A 779 GLN cc_start: 0.7292 (pt0) cc_final: 0.7018 (mt0) REVERT: A 824 GLN cc_start: 0.7875 (tt0) cc_final: 0.7646 (tp-100) REVERT: A 872 LEU cc_start: 0.8576 (tp) cc_final: 0.8316 (tm) REVERT: A 878 GLN cc_start: 0.7582 (tt0) cc_final: 0.6952 (tm-30) REVERT: A 977 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8403 (mp10) REVERT: A 988 ARG cc_start: 0.7706 (mtm110) cc_final: 0.7411 (mmt180) REVERT: A 1082 LYS cc_start: 0.7676 (pttt) cc_final: 0.7443 (pttp) REVERT: A 1138 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8002 (mtm180) REVERT: A 1223 ILE cc_start: 0.7771 (mp) cc_final: 0.7541 (tp) REVERT: A 1243 GLN cc_start: 0.8106 (tt0) cc_final: 0.7866 (pt0) REVERT: A 1491 PRO cc_start: 0.7739 (Cg_exo) cc_final: 0.7427 (Cg_endo) REVERT: A 1492 HIS cc_start: 0.8812 (m90) cc_final: 0.8246 (m-70) REVERT: A 1494 PHE cc_start: 0.8796 (m-80) cc_final: 0.8550 (m-80) REVERT: A 1498 ASP cc_start: 0.8645 (m-30) cc_final: 0.8238 (t0) REVERT: A 1618 PHE cc_start: 0.6862 (OUTLIER) cc_final: 0.6401 (m-80) REVERT: A 1766 PHE cc_start: 0.8199 (m-80) cc_final: 0.7926 (m-80) REVERT: A 1795 ARG cc_start: 0.8032 (mtt180) cc_final: 0.7768 (mpp-170) REVERT: A 1796 MET cc_start: 0.7555 (mmm) cc_final: 0.6958 (mtp) REVERT: A 1801 CYS cc_start: 0.8379 (t) cc_final: 0.8029 (t) outliers start: 16 outliers final: 7 residues processed: 150 average time/residue: 0.9831 time to fit residues: 164.3705 Evaluate side-chains 142 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1618 PHE Chi-restraints excluded: chain A residue 1759 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 HIS A1107 ASN ** A1748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1754 GLN A1826 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.132648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.095578 restraints weight = 50856.311| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.49 r_work: 0.2964 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12589 Z= 0.210 Angle : 0.518 5.051 17150 Z= 0.268 Chirality : 0.039 0.208 1944 Planarity : 0.004 0.039 2098 Dihedral : 9.260 102.300 2365 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.74 % Allowed : 11.94 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 1.84 (0.22), residues: 1470 helix: 2.06 (0.17), residues: 948 sheet: 0.59 (0.69), residues: 54 loop : -0.44 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 376 TYR 0.020 0.001 TYR A1800 PHE 0.020 0.002 PHE A1499 TRP 0.015 0.001 TRP A 625 HIS 0.006 0.001 HIS A1294 Details of bonding type rmsd covalent geometry : bond 0.00490 (12584) covalent geometry : angle 0.51609 (17137) SS BOND : bond 0.00401 ( 2) SS BOND : angle 0.31001 ( 4) hydrogen bonds : bond 0.04871 ( 718) hydrogen bonds : angle 4.16387 ( 2088) link_BETA1-4 : bond 0.00356 ( 2) link_BETA1-4 : angle 2.07518 ( 6) link_NAG-ASN : bond 0.00021 ( 1) link_NAG-ASN : angle 1.62005 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue TYR 558 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue TYR 710 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue SER 714 is missing expected H atoms. Skipping. Residue ILE 742 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue VAL 797 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue TYR 935 is missing expected H atoms. Skipping. Residue TYR 1156 is missing expected H atoms. Skipping. Residue THR 1178 is missing expected H atoms. Skipping. Residue LEU 1179 is missing expected H atoms. Skipping. Residue LEU 1191 is missing expected H atoms. Skipping. Residue TYR 1193 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue LYS 1385 is missing expected H atoms. Skipping. Residue LEU 1414 is missing expected H atoms. Skipping. Residue SER 1415 is missing expected H atoms. Skipping. Residue LEU 1417 is missing expected H atoms. Skipping. Residue ILE 1419 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue VAL 1526 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue MET 1621 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue MET 1694 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue ILE 1769 is missing expected H atoms. Skipping. Residue LEU 1771 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue ILE 1780 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue LYS 1798 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8851 (ptm) REVERT: A 771 HIS cc_start: 0.8149 (m-70) cc_final: 0.7671 (m90) REVERT: A 778 HIS cc_start: 0.7033 (m-70) cc_final: 0.6595 (m-70) REVERT: A 779 GLN cc_start: 0.7329 (pt0) cc_final: 0.6962 (mt0) REVERT: A 824 GLN cc_start: 0.7886 (tt0) cc_final: 0.7652 (tp-100) REVERT: A 872 LEU cc_start: 0.8618 (tp) cc_final: 0.8364 (tm) REVERT: A 878 GLN cc_start: 0.7579 (tt0) cc_final: 0.6955 (tm-30) REVERT: A 977 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8383 (mp10) REVERT: A 988 ARG cc_start: 0.7760 (mtm110) cc_final: 0.7460 (mmt180) REVERT: A 1082 LYS cc_start: 0.7721 (pttt) cc_final: 0.7476 (pttp) REVERT: A 1138 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7923 (mtm180) REVERT: A 1223 ILE cc_start: 0.7865 (mp) cc_final: 0.7566 (tp) REVERT: A 1491 PRO cc_start: 0.7810 (Cg_exo) cc_final: 0.7457 (Cg_endo) REVERT: A 1492 HIS cc_start: 0.8792 (m90) cc_final: 0.8475 (m90) REVERT: A 1498 ASP cc_start: 0.8675 (m-30) cc_final: 0.8235 (t0) REVERT: A 1618 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.6435 (m-80) REVERT: A 1796 MET cc_start: 0.7590 (mmm) cc_final: 0.7022 (mtp) REVERT: A 1801 CYS cc_start: 0.8323 (t) cc_final: 0.8037 (t) outliers start: 21 outliers final: 8 residues processed: 154 average time/residue: 0.9843 time to fit residues: 168.2269 Evaluate side-chains 145 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1618 PHE Chi-restraints excluded: chain A residue 1759 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 65 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 74 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN A1107 ASN A1269 GLN A1754 GLN A1767 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.134178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.097274 restraints weight = 50300.888| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.49 r_work: 0.2998 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12589 Z= 0.117 Angle : 0.474 5.311 17150 Z= 0.243 Chirality : 0.037 0.211 1944 Planarity : 0.004 0.049 2098 Dihedral : 8.694 88.134 2365 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.33 % Allowed : 12.35 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.22), residues: 1470 helix: 2.24 (0.17), residues: 944 sheet: 0.21 (0.64), residues: 64 loop : -0.35 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1795 TYR 0.019 0.001 TYR A1800 PHE 0.020 0.001 PHE A1499 TRP 0.013 0.001 TRP A 625 HIS 0.003 0.001 HIS A1013 Details of bonding type rmsd covalent geometry : bond 0.00258 (12584) covalent geometry : angle 0.47241 (17137) SS BOND : bond 0.00286 ( 2) SS BOND : angle 0.35854 ( 4) hydrogen bonds : bond 0.04338 ( 718) hydrogen bonds : angle 4.03547 ( 2088) link_BETA1-4 : bond 0.00312 ( 2) link_BETA1-4 : angle 1.81932 ( 6) link_NAG-ASN : bond 0.00264 ( 1) link_NAG-ASN : angle 1.41839 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue TYR 558 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue TYR 710 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue SER 714 is missing expected H atoms. Skipping. Residue ILE 742 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue VAL 797 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue TYR 935 is missing expected H atoms. Skipping. Residue TYR 1156 is missing expected H atoms. Skipping. Residue THR 1178 is missing expected H atoms. Skipping. Residue LEU 1179 is missing expected H atoms. Skipping. Residue LEU 1191 is missing expected H atoms. Skipping. Residue TYR 1193 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue LYS 1385 is missing expected H atoms. Skipping. Residue LEU 1414 is missing expected H atoms. Skipping. Residue SER 1415 is missing expected H atoms. Skipping. Residue LEU 1417 is missing expected H atoms. Skipping. Residue ILE 1419 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue VAL 1526 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue MET 1621 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue MET 1694 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue ILE 1769 is missing expected H atoms. Skipping. Residue LEU 1771 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue ILE 1780 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue LYS 1798 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7428 (mp0) REVERT: A 771 HIS cc_start: 0.8142 (m-70) cc_final: 0.7520 (m90) REVERT: A 778 HIS cc_start: 0.6969 (m-70) cc_final: 0.6521 (m-70) REVERT: A 779 GLN cc_start: 0.7313 (pt0) cc_final: 0.6987 (mt0) REVERT: A 824 GLN cc_start: 0.7849 (tt0) cc_final: 0.7627 (tp-100) REVERT: A 872 LEU cc_start: 0.8640 (tp) cc_final: 0.8411 (tm) REVERT: A 878 GLN cc_start: 0.7577 (tt0) cc_final: 0.6949 (tm-30) REVERT: A 977 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8302 (mp10) REVERT: A 988 ARG cc_start: 0.7722 (mtm110) cc_final: 0.7436 (mmt180) REVERT: A 1082 LYS cc_start: 0.7693 (pttt) cc_final: 0.7457 (pttp) REVERT: A 1138 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7903 (mtm180) REVERT: A 1223 ILE cc_start: 0.7745 (mp) cc_final: 0.7535 (tp) REVERT: A 1491 PRO cc_start: 0.7817 (Cg_exo) cc_final: 0.7415 (Cg_endo) REVERT: A 1492 HIS cc_start: 0.8798 (m90) cc_final: 0.8462 (m90) REVERT: A 1498 ASP cc_start: 0.8685 (m-30) cc_final: 0.8213 (t0) REVERT: A 1618 PHE cc_start: 0.6905 (OUTLIER) cc_final: 0.6460 (m-80) REVERT: A 1766 PHE cc_start: 0.8122 (m-80) cc_final: 0.7876 (m-80) REVERT: A 1796 MET cc_start: 0.7627 (mmm) cc_final: 0.7024 (mtp) REVERT: A 1801 CYS cc_start: 0.8193 (t) cc_final: 0.7837 (t) outliers start: 16 outliers final: 6 residues processed: 149 average time/residue: 0.9964 time to fit residues: 165.2383 Evaluate side-chains 141 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1618 PHE Chi-restraints excluded: chain A residue 1759 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 133 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN A 563 HIS A1107 ASN ** A1748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.132991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.095892 restraints weight = 50381.990| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.49 r_work: 0.2972 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12589 Z= 0.191 Angle : 0.506 6.619 17150 Z= 0.260 Chirality : 0.038 0.207 1944 Planarity : 0.004 0.043 2098 Dihedral : 8.487 80.586 2365 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.24 % Allowed : 12.69 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.00 (0.22), residues: 1470 helix: 2.23 (0.17), residues: 941 sheet: 0.18 (0.64), residues: 64 loop : -0.37 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 376 TYR 0.019 0.001 TYR A1800 PHE 0.021 0.001 PHE A1499 TRP 0.014 0.001 TRP A 625 HIS 0.005 0.001 HIS A1294 Details of bonding type rmsd covalent geometry : bond 0.00443 (12584) covalent geometry : angle 0.50503 (17137) SS BOND : bond 0.00370 ( 2) SS BOND : angle 0.34034 ( 4) hydrogen bonds : bond 0.04643 ( 718) hydrogen bonds : angle 4.07271 ( 2088) link_BETA1-4 : bond 0.00342 ( 2) link_BETA1-4 : angle 1.87282 ( 6) link_NAG-ASN : bond 0.00050 ( 1) link_NAG-ASN : angle 1.52345 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue TYR 558 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue TYR 710 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue SER 714 is missing expected H atoms. Skipping. Residue ILE 742 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue VAL 797 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue TYR 935 is missing expected H atoms. Skipping. Residue TYR 1156 is missing expected H atoms. Skipping. Residue THR 1178 is missing expected H atoms. Skipping. Residue LEU 1179 is missing expected H atoms. Skipping. Residue LEU 1191 is missing expected H atoms. Skipping. Residue TYR 1193 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue LYS 1385 is missing expected H atoms. Skipping. Residue LEU 1414 is missing expected H atoms. Skipping. Residue SER 1415 is missing expected H atoms. Skipping. Residue LEU 1417 is missing expected H atoms. Skipping. Residue ILE 1419 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue VAL 1526 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue MET 1621 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue MET 1694 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue ILE 1769 is missing expected H atoms. Skipping. Residue LEU 1771 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue ILE 1780 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue LYS 1798 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8845 (ptm) REVERT: A 346 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7453 (mp0) REVERT: A 771 HIS cc_start: 0.8167 (m-70) cc_final: 0.7584 (m90) REVERT: A 778 HIS cc_start: 0.7106 (m-70) cc_final: 0.6664 (m-70) REVERT: A 779 GLN cc_start: 0.7274 (pt0) cc_final: 0.6968 (mt0) REVERT: A 824 GLN cc_start: 0.7860 (tt0) cc_final: 0.7637 (tp-100) REVERT: A 872 LEU cc_start: 0.8640 (tp) cc_final: 0.8417 (tm) REVERT: A 878 GLN cc_start: 0.7581 (tt0) cc_final: 0.6950 (tm-30) REVERT: A 977 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8293 (mp10) REVERT: A 988 ARG cc_start: 0.7753 (mtm110) cc_final: 0.7461 (mmt180) REVERT: A 1082 LYS cc_start: 0.7706 (pttt) cc_final: 0.7466 (pttp) REVERT: A 1138 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7887 (mtm180) REVERT: A 1223 ILE cc_start: 0.7794 (mp) cc_final: 0.7539 (tp) REVERT: A 1491 PRO cc_start: 0.7804 (Cg_exo) cc_final: 0.7444 (Cg_endo) REVERT: A 1492 HIS cc_start: 0.8791 (m90) cc_final: 0.8453 (m90) REVERT: A 1498 ASP cc_start: 0.8726 (m-30) cc_final: 0.8252 (t0) REVERT: A 1618 PHE cc_start: 0.6917 (OUTLIER) cc_final: 0.6479 (m-80) REVERT: A 1766 PHE cc_start: 0.8213 (m-80) cc_final: 0.7919 (m-80) REVERT: A 1796 MET cc_start: 0.7664 (mmm) cc_final: 0.7060 (mtp) outliers start: 15 outliers final: 5 residues processed: 144 average time/residue: 1.0486 time to fit residues: 167.9304 Evaluate side-chains 139 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1618 PHE Chi-restraints excluded: chain A residue 1759 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 65 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1107 ASN ** A1754 GLN ** 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 = 0.3773 r_free = 0.3773 target = 0.134167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.097213 restraints weight = 50282.487| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.50 r_work: 0.2999 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12589 Z= 0.123 Angle : 0.473 4.955 17150 Z= 0.242 Chirality : 0.037 0.208 1944 Planarity : 0.004 0.039 2098 Dihedral : 8.207 79.458 2365 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.83 % Allowed : 13.43 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.14 (0.22), residues: 1470 helix: 2.35 (0.17), residues: 940 sheet: 0.21 (0.64), residues: 64 loop : -0.35 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1795 TYR 0.020 0.001 TYR A1800 PHE 0.022 0.001 PHE A1499 TRP 0.012 0.001 TRP A 625 HIS 0.002 0.001 HIS A1013 Details of bonding type rmsd covalent geometry : bond 0.00276 (12584) covalent geometry : angle 0.47206 (17137) SS BOND : bond 0.00281 ( 2) SS BOND : angle 0.34821 ( 4) hydrogen bonds : bond 0.04289 ( 718) hydrogen bonds : angle 3.98496 ( 2088) link_BETA1-4 : bond 0.00298 ( 2) link_BETA1-4 : angle 1.72378 ( 6) link_NAG-ASN : bond 0.00227 ( 1) link_NAG-ASN : angle 1.38372 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue TYR 558 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue TYR 710 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue SER 714 is missing expected H atoms. Skipping. Residue ILE 742 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue VAL 797 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue TYR 935 is missing expected H atoms. Skipping. Residue TYR 1156 is missing expected H atoms. Skipping. Residue THR 1178 is missing expected H atoms. Skipping. Residue LEU 1179 is missing expected H atoms. Skipping. Residue LEU 1191 is missing expected H atoms. Skipping. Residue TYR 1193 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue LYS 1385 is missing expected H atoms. Skipping. Residue LEU 1414 is missing expected H atoms. Skipping. Residue SER 1415 is missing expected H atoms. Skipping. Residue LEU 1417 is missing expected H atoms. Skipping. Residue ILE 1419 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue VAL 1526 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue MET 1621 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue MET 1694 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue ILE 1769 is missing expected H atoms. Skipping. Residue LEU 1771 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue ILE 1780 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue LYS 1798 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8807 (ptm) REVERT: A 346 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8062 (pt0) REVERT: A 771 HIS cc_start: 0.8133 (m-70) cc_final: 0.7487 (m90) REVERT: A 778 HIS cc_start: 0.7066 (m-70) cc_final: 0.6596 (m-70) REVERT: A 779 GLN cc_start: 0.7316 (pt0) cc_final: 0.6971 (mt0) REVERT: A 791 ARG cc_start: 0.8050 (ttp80) cc_final: 0.7775 (ttp80) REVERT: A 824 GLN cc_start: 0.7854 (tt0) cc_final: 0.7636 (tp-100) REVERT: A 872 LEU cc_start: 0.8637 (tp) cc_final: 0.8417 (tm) REVERT: A 878 GLN cc_start: 0.7581 (tt0) cc_final: 0.6953 (tm-30) REVERT: A 977 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8265 (mp10) REVERT: A 988 ARG cc_start: 0.7727 (mtm110) cc_final: 0.7443 (mmt180) REVERT: A 1082 LYS cc_start: 0.7696 (pttt) cc_final: 0.7457 (pttp) REVERT: A 1138 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7914 (mtm180) REVERT: A 1223 ILE cc_start: 0.7777 (mp) cc_final: 0.7523 (tp) REVERT: A 1491 PRO cc_start: 0.7747 (Cg_exo) cc_final: 0.7393 (Cg_endo) REVERT: A 1492 HIS cc_start: 0.8758 (m90) cc_final: 0.8403 (m90) REVERT: A 1498 ASP cc_start: 0.8723 (m-30) cc_final: 0.8192 (t0) REVERT: A 1618 PHE cc_start: 0.6900 (OUTLIER) cc_final: 0.6465 (m-80) REVERT: A 1766 PHE cc_start: 0.8225 (m-80) cc_final: 0.7929 (m-80) REVERT: A 1796 MET cc_start: 0.7664 (mmm) cc_final: 0.7074 (mtp) REVERT: A 1801 CYS cc_start: 0.8186 (t) cc_final: 0.7841 (t) outliers start: 10 outliers final: 5 residues processed: 141 average time/residue: 1.1052 time to fit residues: 172.4969 Evaluate side-chains 142 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1618 PHE Chi-restraints excluded: chain A residue 1759 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 58 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN A1107 ASN A1754 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.133842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.096885 restraints weight = 50321.007| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.49 r_work: 0.2988 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12589 Z= 0.144 Angle : 0.482 6.441 17150 Z= 0.247 Chirality : 0.037 0.207 1944 Planarity : 0.004 0.039 2098 Dihedral : 8.086 83.386 2365 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.91 % Allowed : 13.35 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.16 (0.22), residues: 1470 helix: 2.37 (0.17), residues: 940 sheet: 0.20 (0.65), residues: 64 loop : -0.34 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1795 TYR 0.019 0.001 TYR A1800 PHE 0.022 0.001 PHE A1499 TRP 0.013 0.001 TRP A 625 HIS 0.004 0.001 HIS A1294 Details of bonding type rmsd covalent geometry : bond 0.00332 (12584) covalent geometry : angle 0.48114 (17137) SS BOND : bond 0.00309 ( 2) SS BOND : angle 0.33697 ( 4) hydrogen bonds : bond 0.04334 ( 718) hydrogen bonds : angle 3.96956 ( 2088) link_BETA1-4 : bond 0.00315 ( 2) link_BETA1-4 : angle 1.73729 ( 6) link_NAG-ASN : bond 0.00152 ( 1) link_NAG-ASN : angle 1.44595 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue TYR 558 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue TYR 710 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue SER 714 is missing expected H atoms. Skipping. Residue ILE 742 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue VAL 797 is missing expected H atoms. Skipping. Residue LYS 892 is missing expected H atoms. Skipping. Residue TYR 935 is missing expected H atoms. Skipping. Residue TYR 1156 is missing expected H atoms. Skipping. Residue THR 1178 is missing expected H atoms. Skipping. Residue LEU 1179 is missing expected H atoms. Skipping. Residue LEU 1191 is missing expected H atoms. Skipping. Residue TYR 1193 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue LYS 1385 is missing expected H atoms. Skipping. Residue LEU 1414 is missing expected H atoms. Skipping. Residue SER 1415 is missing expected H atoms. Skipping. Residue LEU 1417 is missing expected H atoms. Skipping. Residue ILE 1419 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue VAL 1526 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue MET 1621 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue MET 1694 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue ILE 1769 is missing expected H atoms. Skipping. Residue LEU 1771 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue ILE 1780 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue LYS 1798 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8787 (ptm) REVERT: A 346 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8092 (pt0) REVERT: A 771 HIS cc_start: 0.8140 (m-70) cc_final: 0.7490 (m90) REVERT: A 779 GLN cc_start: 0.7321 (pt0) cc_final: 0.6974 (mt0) REVERT: A 824 GLN cc_start: 0.7838 (tt0) cc_final: 0.7612 (tp-100) REVERT: A 872 LEU cc_start: 0.8627 (tp) cc_final: 0.8414 (tm) REVERT: A 878 GLN cc_start: 0.7579 (tt0) cc_final: 0.6949 (tm-30) REVERT: A 977 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8279 (mp10) REVERT: A 988 ARG cc_start: 0.7737 (mtm110) cc_final: 0.7460 (mmt180) REVERT: A 1082 LYS cc_start: 0.7701 (pttt) cc_final: 0.7464 (pttp) REVERT: A 1138 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7868 (mtm180) REVERT: A 1223 ILE cc_start: 0.7800 (mp) cc_final: 0.7543 (tp) REVERT: A 1491 PRO cc_start: 0.7766 (Cg_exo) cc_final: 0.7420 (Cg_endo) REVERT: A 1492 HIS cc_start: 0.8760 (m90) cc_final: 0.8399 (m90) REVERT: A 1498 ASP cc_start: 0.8747 (m-30) cc_final: 0.8231 (t0) REVERT: A 1500 PHE cc_start: 0.8349 (m-10) cc_final: 0.8121 (m-10) REVERT: A 1618 PHE cc_start: 0.6897 (OUTLIER) cc_final: 0.6468 (m-80) REVERT: A 1796 MET cc_start: 0.7670 (mmm) cc_final: 0.7073 (mtp) REVERT: A 1801 CYS cc_start: 0.8175 (t) cc_final: 0.7914 (t) outliers start: 11 outliers final: 5 residues processed: 137 average time/residue: 1.0011 time to fit residues: 152.2231 Evaluate side-chains 140 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1618 PHE Chi-restraints excluded: chain A residue 1619 PHE Chi-restraints excluded: chain A residue 1759 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 98 optimal weight: 3.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN A1754 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.133524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.096593 restraints weight = 50305.158| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.49 r_work: 0.2984 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12589 Z= 0.153 Angle : 0.484 4.912 17150 Z= 0.248 Chirality : 0.037 0.203 1944 Planarity : 0.004 0.039 2098 Dihedral : 8.052 82.135 2365 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.66 % Allowed : 13.85 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 2.17 (0.22), residues: 1470 helix: 2.37 (0.17), residues: 940 sheet: 0.30 (0.65), residues: 64 loop : -0.34 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1795 TYR 0.020 0.001 TYR A1800 PHE 0.020 0.001 PHE A1499 TRP 0.013 0.001 TRP A 625 HIS 0.003 0.001 HIS A1013 Details of bonding type rmsd covalent geometry : bond 0.00353 (12584) covalent geometry : angle 0.48306 (17137) SS BOND : bond 0.00320 ( 2) SS BOND : angle 0.32738 ( 4) hydrogen bonds : bond 0.04374 ( 718) hydrogen bonds : angle 3.97103 ( 2088) link_BETA1-4 : bond 0.00349 ( 2) link_BETA1-4 : angle 1.70619 ( 6) link_NAG-ASN : bond 0.00115 ( 1) link_NAG-ASN : angle 1.38501 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7869.80 seconds wall clock time: 133 minutes 45.10 seconds (8025.10 seconds total)