Starting phenix.real_space_refine on Fri Aug 7 11:27:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p1m_17354/08_2026/8p1m_17354_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p1m_17354/08_2026/8p1m_17354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p1m_17354/08_2026/8p1m_17354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p1m_17354/08_2026/8p1m_17354.map" model { file = "/net/cci-nas-00/data/ceres_data/8p1m_17354/08_2026/8p1m_17354_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p1m_17354/08_2026/8p1m_17354_trim.cif" } resolution = 3.23 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= 0.042 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: 7 Type Number sf(0) Gaussians P 8 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 6784 2.51 5 N 1781 2.21 5 O 1965 1.98 5 H 10539 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21135 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 20938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1298, 20938 Classifications: {'peptide': 1298} Link IDs: {'PTRANS': 42, 'TRANS': 1255} Chain breaks: 4 Chain: "D" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 164 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.89, per 1000 atoms: 0.14 Number of scatterers: 21135 At special positions: 0 Unit cell: (89.472, 103.452, 127.684, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 56 16.00 P 8 15.00 Mg 2 11.99 O 1965 8.00 N 1781 7.00 C 6784 6.00 H 10539 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 498.4 milliseconds 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 8 sheets defined 56.4% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 239 through 251 removed outlier: 3.784A pdb=" N LEU A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 282 removed outlier: 3.672A pdb=" N CYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 removed outlier: 3.756A pdb=" N GLN A 311 " --> pdb=" O THR A 307 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 409 through 427 removed outlier: 3.857A pdb=" N GLN A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 470 through 489 removed outlier: 3.517A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N HIS A 477 " --> pdb=" O TRP A 473 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 592 removed outlier: 3.502A pdb=" N GLU A 590 " --> pdb=" O GLN A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 614 removed outlier: 3.771A pdb=" N ARG A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 603 " --> pdb=" O TYR A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 634 removed outlier: 3.905A pdb=" N CYS A 620 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG A 627 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR A 628 " --> pdb=" O ASP A 624 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 639 through 648 Processing helix chain 'A' and resid 656 through 675 removed outlier: 3.799A pdb=" N GLN A 673 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 726 removed outlier: 3.993A pdb=" N LEU A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 758 removed outlier: 3.606A pdb=" N GLU A 737 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 744 " --> pdb=" O LYS A 740 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 765 removed outlier: 3.583A pdb=" N VAL A 764 " --> pdb=" O GLY A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 775 removed outlier: 3.648A pdb=" N ALA A 775 " --> pdb=" O TRP A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 798 Processing helix chain 'A' and resid 804 through 815 Processing helix chain 'A' and resid 848 through 859 Processing helix chain 'A' and resid 866 through 873 removed outlier: 3.720A pdb=" N GLU A 871 " --> pdb=" O LYS A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 917 removed outlier: 3.706A pdb=" N ALA A 914 " --> pdb=" O ASP A 910 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 915 " --> pdb=" O TYR A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 947 removed outlier: 3.745A pdb=" N GLY A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 992 removed outlier: 3.997A pdb=" N ARG A 987 " --> pdb=" O ALA A 983 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET A 991 " --> pdb=" O ARG A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1020 through 1028 Processing helix chain 'A' and resid 1034 through 1042 removed outlier: 3.523A pdb=" N GLN A1039 " --> pdb=" O PRO A1035 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE A1040 " --> pdb=" O HIS A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1084 Processing helix chain 'A' and resid 1113 through 1127 Processing helix chain 'A' and resid 1128 through 1134 removed outlier: 3.609A pdb=" N TRP A1131 " --> pdb=" O HIS A1128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A1132 " --> pdb=" O LEU A1129 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A1133 " --> pdb=" O HIS A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1152 removed outlier: 3.945A pdb=" N SER A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A1142 " --> pdb=" O MET A1138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A1143 " --> pdb=" O TRP A1139 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1175 removed outlier: 3.711A pdb=" N THR A1174 " --> pdb=" O GLU A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1190 removed outlier: 3.871A pdb=" N ILE A1188 " --> pdb=" O PRO A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1218 removed outlier: 3.837A pdb=" N ALA A1207 " --> pdb=" O ASP A1203 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A1209 " --> pdb=" O LEU A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1241 removed outlier: 3.502A pdb=" N ALA A1228 " --> pdb=" O VAL A1224 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A1229 " --> pdb=" O ALA A1225 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A1230 " --> pdb=" O GLN A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1254 removed outlier: 3.909A pdb=" N TYR A1253 " --> pdb=" O HIS A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1261 removed outlier: 3.526A pdb=" N THR A1261 " --> pdb=" O HIS A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1266 Processing helix chain 'A' and resid 1272 through 1279 Processing helix chain 'A' and resid 1282 through 1299 removed outlier: 3.832A pdb=" N LYS A1286 " --> pdb=" O GLY A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1304 No H-bonds generated for 'chain 'A' and resid 1302 through 1304' Processing helix chain 'A' and resid 1305 through 1319 Processing helix chain 'A' and resid 1356 through 1365 removed outlier: 3.620A pdb=" N SER A1362 " --> pdb=" O LEU A1358 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A1363 " --> pdb=" O GLU A1359 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1370 Processing helix chain 'A' and resid 1375 through 1388 removed outlier: 3.740A pdb=" N ILE A1381 " --> pdb=" O ASP A1377 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR A1382 " --> pdb=" O ASN A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1396 Processing helix chain 'A' and resid 1400 through 1412 removed outlier: 4.025A pdb=" N GLN A1409 " --> pdb=" O ARG A1405 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA A1410 " --> pdb=" O PHE A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1439 removed outlier: 3.502A pdb=" N LEU A1430 " --> pdb=" O PHE A1426 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A1431 " --> pdb=" O ARG A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1454 Processing helix chain 'A' and resid 1502 through 1511 Processing helix chain 'A' and resid 1514 through 1525 Processing helix chain 'A' and resid 1530 through 1546 removed outlier: 3.839A pdb=" N ARG A1544 " --> pdb=" O ASP A1540 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A1545 " --> pdb=" O GLY A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1568 removed outlier: 4.079A pdb=" N ILE A1559 " --> pdb=" O VAL A1555 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A1560 " --> pdb=" O MET A1556 " (cutoff:3.500A) Proline residue: A1561 - end of helix Processing helix chain 'A' and resid 1581 through 1592 Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261 removed outlier: 4.376A pdb=" N THR A1163 " --> pdb=" O SER A 970 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A1100 " --> pdb=" O ALA A 971 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 503 removed outlier: 3.688A pdb=" N VAL A 508 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 531 " --> pdb=" O GLY A 555 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 499 through 503 removed outlier: 3.688A pdb=" N VAL A 508 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 527 " --> pdb=" O MET A 560 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AA5, first strand: chain 'A' and resid 832 through 837 removed outlier: 5.625A pdb=" N SER A 844 " --> pdb=" O GLY A 835 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 892 through 897 removed outlier: 4.322A pdb=" N ARG A 892 " --> pdb=" O LYS A 884 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA A 877 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE A 881 " --> pdb=" O PHE A1018 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 949 through 953 Processing sheet with id=AA8, first strand: chain 'A' and resid 1486 through 1491 removed outlier: 3.888A pdb=" N ARG A1570 " --> pdb=" O PHE A1490 " (cutoff:3.500A) 507 hydrogen bonds defined for protein. 1467 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: 5.03 Time building geometry restraints manager: 1.97 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: 10522 1.03 - 1.23: 25 1.23 - 1.42: 4597 1.42 - 1.62: 6141 1.62 - 1.81: 95 Bond restraints: 21380 Sorted by residual: bond pdb=" CB PRO A1184 " pdb=" CG PRO A1184 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.24e+00 bond pdb=" N VAL A1181 " pdb=" CA VAL A1181 " ideal model delta sigma weight residual 1.474 1.455 0.020 1.57e-02 4.06e+03 1.57e+00 bond pdb=" C SER A 977 " pdb=" N PRO A 978 " ideal model delta sigma weight residual 1.335 1.349 -0.015 1.28e-02 6.10e+03 1.29e+00 bond pdb=" CB VAL A1181 " pdb=" CG2 VAL A1181 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" CA VAL A1181 " pdb=" C VAL A1181 " ideal model delta sigma weight residual 1.524 1.516 0.009 8.60e-03 1.35e+04 9.99e-01 ... (remaining 21375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 37368 1.29 - 2.59: 1139 2.59 - 3.88: 80 3.88 - 5.18: 16 5.18 - 6.47: 8 Bond angle restraints: 38611 Sorted by residual: angle pdb=" N GLU A 590 " pdb=" CA GLU A 590 " pdb=" C GLU A 590 " ideal model delta sigma weight residual 114.75 108.68 6.07 1.26e+00 6.30e-01 2.32e+01 angle pdb=" N VAL A 800 " pdb=" CA VAL A 800 " pdb=" C VAL A 800 " ideal model delta sigma weight residual 113.53 108.97 4.56 9.80e-01 1.04e+00 2.16e+01 angle pdb=" C SER A1097 " pdb=" CA SER A1097 " pdb=" CB SER A1097 " ideal model delta sigma weight residual 117.23 111.78 5.45 1.36e+00 5.41e-01 1.60e+01 angle pdb=" O5' G D 6 " pdb=" C5' G D 6 " pdb=" C4' G D 6 " ideal model delta sigma weight residual 109.40 111.94 -2.54 8.00e-01 1.56e+00 1.01e+01 angle pdb=" N VAL A1012 " pdb=" CA VAL A1012 " pdb=" C VAL A1012 " ideal model delta sigma weight residual 112.29 109.33 2.96 9.40e-01 1.13e+00 9.92e+00 ... (remaining 38606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9098 17.92 - 35.83: 727 35.83 - 53.75: 187 53.75 - 71.67: 48 71.67 - 89.58: 8 Dihedral angle restraints: 10068 sinusoidal: 5460 harmonic: 4608 Sorted by residual: dihedral pdb=" CA SER A1182 " pdb=" C SER A1182 " pdb=" N ILE A1183 " pdb=" CA ILE A1183 " ideal model delta harmonic sigma weight residual 180.00 143.44 36.56 0 5.00e+00 4.00e-02 5.35e+01 dihedral pdb=" CA ILE A1183 " pdb=" C ILE A1183 " pdb=" N PRO A1184 " pdb=" CA PRO A1184 " ideal model delta harmonic sigma weight residual -180.00 -153.06 -26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA HIS A 732 " pdb=" C HIS A 732 " pdb=" N GLY A 733 " pdb=" CA GLY A 733 " ideal model delta harmonic sigma weight residual -180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 10065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1446 0.057 - 0.115: 167 0.115 - 0.172: 19 0.172 - 0.230: 0 0.230 - 0.287: 3 Chirality restraints: 1635 Sorted by residual: chirality pdb=" C2' ATP A2201 " pdb=" C1' ATP A2201 " pdb=" C3' ATP A2201 " pdb=" O2' ATP A2201 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C3' ATP A2201 " pdb=" C2' ATP A2201 " pdb=" C4' ATP A2201 " pdb=" O3' ATP A2201 " both_signs ideal model delta sigma weight residual False -2.63 -2.90 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C4' ATP A2201 " pdb=" C3' ATP A2201 " pdb=" C5' ATP A2201 " pdb=" O4' ATP A2201 " both_signs ideal model delta sigma weight residual False -2.49 -2.76 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1632 not shown) Planarity restraints: 3081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1183 " -0.081 5.00e-02 4.00e+02 1.23e-01 2.41e+01 pdb=" N PRO A1184 " 0.212 5.00e-02 4.00e+02 pdb=" CA PRO A1184 " -0.067 5.00e-02 4.00e+02 pdb=" CD PRO A1184 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 313 " 0.007 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" C ASP A 313 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP A 313 " 0.009 2.00e-02 2.50e+03 pdb=" N SER A 314 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1183 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.65e+00 pdb=" C ILE A1183 " 0.022 2.00e-02 2.50e+03 pdb=" O ILE A1183 " -0.008 2.00e-02 2.50e+03 pdb=" N PRO A1184 " -0.008 2.00e-02 2.50e+03 ... (remaining 3078 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 793 2.17 - 2.77: 42198 2.77 - 3.38: 59821 3.38 - 3.99: 77488 3.99 - 4.60: 123291 Nonbonded interactions: 303591 Sorted by model distance: nonbonded pdb=" HE2 HIS A 732 " pdb=" O THR A 888 " model vdw 1.558 2.450 nonbonded pdb=" O ASP A 972 " pdb=" H SER A1158 " model vdw 1.581 2.450 nonbonded pdb=" HH TYR A 710 " pdb=" OE2 GLU A 719 " model vdw 1.589 2.450 nonbonded pdb=" OE2 GLU A 275 " pdb=" HH TYR A 661 " model vdw 1.606 2.450 nonbonded pdb=" O SER A1133 " pdb=" HG SER A1141 " model vdw 1.619 2.450 ... (remaining 303586 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: 2.000 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: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.990 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10841 Z= 0.148 Angle : 0.544 6.474 14678 Z= 0.312 Chirality : 0.039 0.287 1635 Planarity : 0.004 0.123 1826 Dihedral : 14.935 89.584 4057 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.07 % Favored : 92.62 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.24), residues: 1288 helix: 0.45 (0.21), residues: 692 sheet: -1.13 (0.48), residues: 106 loop : -1.87 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1418 TYR 0.016 0.001 TYR A1026 PHE 0.016 0.001 PHE A 585 TRP 0.018 0.001 TRP A 498 HIS 0.011 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (10841) covalent geometry : angle 0.54414 / 0.31 (14678) hydrogen bonds : bond 0.16271 / 10.64 ( 498) hydrogen bonds : angle 6.20072 / 4.31 ( 1467) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.8022 (mp) cc_final: 0.7742 (tp) REVERT: A 1357 PHE cc_start: 0.8057 (t80) cc_final: 0.7623 (t80) REVERT: A 1408 MET cc_start: 0.6817 (tpt) cc_final: 0.6576 (tpt) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2437 time to fit residues: 47.1770 Evaluate side-chains 125 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1060 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.158864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.117156 restraints weight = 32307.147| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.93 r_work: 0.3143 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.0592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10841 Z= 0.149 Angle : 0.531 7.648 14678 Z= 0.290 Chirality : 0.037 0.137 1635 Planarity : 0.004 0.128 1826 Dihedral : 8.163 63.745 1515 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.29 % Favored : 93.40 % Rotamer: Outliers : 0.35 % Allowed : 3.83 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.24), residues: 1288 helix: 0.52 (0.20), residues: 699 sheet: -1.40 (0.45), residues: 118 loop : -1.93 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1418 TYR 0.016 0.001 TYR A1026 PHE 0.016 0.001 PHE A 585 TRP 0.008 0.001 TRP A 473 HIS 0.014 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (10841) covalent geometry : angle 0.53070 / 0.29 (14678) hydrogen bonds : bond 0.05356 / 3.53 ( 498) hydrogen bonds : angle 5.01640 / 3.54 ( 1467) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7592 (mp) cc_final: 0.7201 (tp) REVERT: A 563 ASP cc_start: 0.8673 (p0) cc_final: 0.8311 (p0) REVERT: A 929 GLU cc_start: 0.7147 (pp20) cc_final: 0.6326 (pp20) REVERT: A 1408 MET cc_start: 0.6512 (tpt) cc_final: 0.6270 (tpt) outliers start: 4 outliers final: 3 residues processed: 128 average time/residue: 0.2419 time to fit residues: 43.3786 Evaluate side-chains 127 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1315 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 66 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.173874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.136069 restraints weight = 31907.733| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.72 r_work: 0.3159 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10841 Z= 0.177 Angle : 0.529 8.137 14678 Z= 0.285 Chirality : 0.037 0.145 1635 Planarity : 0.004 0.130 1826 Dihedral : 8.030 63.832 1515 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.99 % Favored : 92.70 % Rotamer: Outliers : 0.26 % Allowed : 5.22 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.23), residues: 1288 helix: 0.47 (0.20), residues: 697 sheet: -1.37 (0.46), residues: 116 loop : -1.99 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1418 TYR 0.015 0.001 TYR A1026 PHE 0.015 0.001 PHE A 585 TRP 0.010 0.001 TRP A 473 HIS 0.012 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (10841) covalent geometry : angle 0.52906 / 0.29 (14678) hydrogen bonds : bond 0.04745 / 3.12 ( 498) hydrogen bonds : angle 4.83977 / 3.42 ( 1467) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7693 (mp) cc_final: 0.7330 (tp) REVERT: A 563 ASP cc_start: 0.8704 (p0) cc_final: 0.8467 (p0) REVERT: A 929 GLU cc_start: 0.7168 (pp20) cc_final: 0.6347 (pp20) REVERT: A 1408 MET cc_start: 0.6617 (tpt) cc_final: 0.6345 (tpt) outliers start: 3 outliers final: 2 residues processed: 126 average time/residue: 0.2554 time to fit residues: 44.8949 Evaluate side-chains 125 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 1315 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 126 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.173335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.135245 restraints weight = 31999.291| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.74 r_work: 0.3152 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10841 Z= 0.177 Angle : 0.523 8.044 14678 Z= 0.282 Chirality : 0.037 0.139 1635 Planarity : 0.004 0.129 1826 Dihedral : 7.955 63.841 1515 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.45 % Favored : 92.24 % Rotamer: Outliers : 0.35 % Allowed : 6.17 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.23), residues: 1288 helix: 0.48 (0.20), residues: 701 sheet: -1.47 (0.45), residues: 118 loop : -2.05 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1418 TYR 0.011 0.001 TYR A1026 PHE 0.016 0.001 PHE A 585 TRP 0.010 0.001 TRP A 473 HIS 0.012 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (10841) covalent geometry : angle 0.52260 / 0.28 (14678) hydrogen bonds : bond 0.04403 / 2.89 ( 498) hydrogen bonds : angle 4.72185 / 3.34 ( 1467) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7688 (mp) cc_final: 0.7346 (tp) REVERT: A 929 GLU cc_start: 0.7151 (pp20) cc_final: 0.6245 (pp20) REVERT: A 1408 MET cc_start: 0.6657 (tpt) cc_final: 0.6410 (tpt) outliers start: 4 outliers final: 3 residues processed: 125 average time/residue: 0.2513 time to fit residues: 44.3613 Evaluate side-chains 125 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 1046 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 24 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.173102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.135075 restraints weight = 31875.603| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.72 r_work: 0.3149 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10841 Z= 0.175 Angle : 0.523 7.833 14678 Z= 0.280 Chirality : 0.037 0.148 1635 Planarity : 0.004 0.127 1826 Dihedral : 7.868 63.828 1515 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.99 % Favored : 92.70 % Rotamer: Outliers : 0.61 % Allowed : 7.39 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.23), residues: 1288 helix: 0.54 (0.20), residues: 702 sheet: -1.43 (0.45), residues: 116 loop : -2.04 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1418 TYR 0.010 0.001 TYR A 869 PHE 0.016 0.001 PHE A 585 TRP 0.010 0.001 TRP A 473 HIS 0.013 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 (10841) covalent geometry : angle 0.52297 / 0.28 (14678) hydrogen bonds : bond 0.04261 / 2.80 ( 498) hydrogen bonds : angle 4.63911 / 3.28 ( 1467) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7670 (mp) cc_final: 0.7327 (tp) REVERT: A 929 GLU cc_start: 0.7179 (pp20) cc_final: 0.6238 (pp20) REVERT: A 1408 MET cc_start: 0.6561 (tpt) cc_final: 0.6323 (tpt) outliers start: 7 outliers final: 3 residues processed: 129 average time/residue: 0.2446 time to fit residues: 44.7294 Evaluate side-chains 129 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 1046 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 47 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.174602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.136744 restraints weight = 31892.949| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.74 r_work: 0.3124 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10841 Z= 0.222 Angle : 0.552 8.011 14678 Z= 0.297 Chirality : 0.038 0.138 1635 Planarity : 0.004 0.128 1826 Dihedral : 7.887 63.831 1515 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.61 % Favored : 92.08 % Rotamer: Outliers : 0.52 % Allowed : 8.17 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.04 (0.23), residues: 1288 helix: 0.40 (0.20), residues: 703 sheet: -1.48 (0.46), residues: 116 loop : -2.13 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 944 TYR 0.014 0.002 TYR A 912 PHE 0.017 0.002 PHE A 585 TRP 0.012 0.001 TRP A 473 HIS 0.013 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.22 (10841) covalent geometry : angle 0.55170 / 0.30 (14678) hydrogen bonds : bond 0.04414 / 2.91 ( 498) hydrogen bonds : angle 4.69369 / 3.32 ( 1467) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7755 (mp) cc_final: 0.7397 (tp) REVERT: A 759 TYR cc_start: 0.6429 (m-80) cc_final: 0.6189 (m-80) REVERT: A 929 GLU cc_start: 0.7315 (pp20) cc_final: 0.6320 (pp20) REVERT: A 1408 MET cc_start: 0.6674 (tpt) cc_final: 0.6249 (tpt) outliers start: 6 outliers final: 5 residues processed: 128 average time/residue: 0.2405 time to fit residues: 43.5853 Evaluate side-chains 128 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1596 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 35 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.181696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.143557 restraints weight = 31632.738| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.78 r_work: 0.3156 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10841 Z= 0.122 Angle : 0.502 7.416 14678 Z= 0.269 Chirality : 0.036 0.140 1635 Planarity : 0.004 0.123 1826 Dihedral : 7.724 63.833 1515 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.98 % Favored : 93.71 % Rotamer: Outliers : 0.26 % Allowed : 8.35 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.24), residues: 1288 helix: 0.65 (0.20), residues: 706 sheet: -1.44 (0.46), residues: 116 loop : -2.00 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 944 TYR 0.026 0.001 TYR A1026 PHE 0.016 0.001 PHE A 585 TRP 0.008 0.001 TRP A 473 HIS 0.012 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (10841) covalent geometry : angle 0.50222 / 0.27 (14678) hydrogen bonds : bond 0.03928 / 2.58 ( 498) hydrogen bonds : angle 4.47433 / 3.16 ( 1467) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7725 (mp) cc_final: 0.7381 (tp) REVERT: A 759 TYR cc_start: 0.6445 (m-80) cc_final: 0.6152 (m-80) REVERT: A 929 GLU cc_start: 0.7294 (pp20) cc_final: 0.6288 (pp20) REVERT: A 1408 MET cc_start: 0.6616 (tpt) cc_final: 0.6183 (tpt) outliers start: 3 outliers final: 2 residues processed: 129 average time/residue: 0.2323 time to fit residues: 42.3945 Evaluate side-chains 128 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 1046 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 93 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.175916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.138070 restraints weight = 31644.324| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.73 r_work: 0.3141 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10841 Z= 0.188 Angle : 0.526 7.189 14678 Z= 0.282 Chirality : 0.037 0.138 1635 Planarity : 0.004 0.122 1826 Dihedral : 7.741 63.835 1515 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.99 % Favored : 92.70 % Rotamer: Outliers : 0.43 % Allowed : 8.70 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.24), residues: 1288 helix: 0.56 (0.20), residues: 705 sheet: -1.56 (0.44), residues: 120 loop : -2.06 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1418 TYR 0.034 0.001 TYR A1026 PHE 0.016 0.001 PHE A 585 TRP 0.010 0.001 TRP A 473 HIS 0.012 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (10841) covalent geometry : angle 0.52604 / 0.28 (14678) hydrogen bonds : bond 0.04097 / 2.70 ( 498) hydrogen bonds : angle 4.52387 / 3.20 ( 1467) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7681 (mp) cc_final: 0.7344 (tp) REVERT: A 759 TYR cc_start: 0.6520 (m-80) cc_final: 0.6262 (m-80) REVERT: A 929 GLU cc_start: 0.7345 (pp20) cc_final: 0.6351 (pp20) outliers start: 5 outliers final: 5 residues processed: 127 average time/residue: 0.2286 time to fit residues: 40.9109 Evaluate side-chains 126 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1596 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 87 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.180696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.142657 restraints weight = 31636.632| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.76 r_work: 0.3144 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10841 Z= 0.162 Angle : 0.518 8.879 14678 Z= 0.277 Chirality : 0.037 0.139 1635 Planarity : 0.004 0.121 1826 Dihedral : 7.692 63.834 1515 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.60 % Favored : 93.09 % Rotamer: Outliers : 0.43 % Allowed : 8.87 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.24), residues: 1288 helix: 0.60 (0.20), residues: 705 sheet: -1.55 (0.44), residues: 120 loop : -2.03 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 944 TYR 0.046 0.001 TYR A1026 PHE 0.016 0.001 PHE A 585 TRP 0.009 0.001 TRP A 473 HIS 0.012 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (10841) covalent geometry : angle 0.51833 / 0.28 (14678) hydrogen bonds : bond 0.03988 / 2.63 ( 498) hydrogen bonds : angle 4.47399 / 3.17 ( 1467) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7669 (mp) cc_final: 0.7334 (tp) REVERT: A 759 TYR cc_start: 0.6585 (m-80) cc_final: 0.6324 (m-80) REVERT: A 929 GLU cc_start: 0.7360 (pp20) cc_final: 0.6373 (pp20) REVERT: A 1408 MET cc_start: 0.6485 (tpt) cc_final: 0.6265 (tpt) outliers start: 5 outliers final: 5 residues processed: 125 average time/residue: 0.2443 time to fit residues: 42.8317 Evaluate side-chains 125 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1596 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 84 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.181416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.143438 restraints weight = 31556.854| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.75 r_work: 0.3157 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10841 Z= 0.135 Angle : 0.499 6.352 14678 Z= 0.268 Chirality : 0.036 0.138 1635 Planarity : 0.004 0.119 1826 Dihedral : 7.593 63.832 1515 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.37 % Favored : 93.32 % Rotamer: Outliers : 0.43 % Allowed : 8.78 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.24), residues: 1288 helix: 0.70 (0.20), residues: 707 sheet: -1.52 (0.45), residues: 120 loop : -1.98 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 944 TYR 0.045 0.001 TYR A1026 PHE 0.016 0.001 PHE A 585 TRP 0.008 0.001 TRP A 473 HIS 0.011 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (10841) covalent geometry : angle 0.49936 / 0.27 (14678) hydrogen bonds : bond 0.03790 / 2.49 ( 498) hydrogen bonds : angle 4.38689 / 3.10 ( 1467) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7661 (mp) cc_final: 0.7329 (tp) REVERT: A 735 MET cc_start: 0.6255 (ttp) cc_final: 0.6023 (ttp) REVERT: A 759 TYR cc_start: 0.6651 (m-80) cc_final: 0.6397 (m-80) REVERT: A 929 GLU cc_start: 0.7352 (pp20) cc_final: 0.6362 (pp20) REVERT: A 1408 MET cc_start: 0.6529 (tpt) cc_final: 0.6187 (tpt) outliers start: 5 outliers final: 5 residues processed: 128 average time/residue: 0.2396 time to fit residues: 43.2351 Evaluate side-chains 125 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1596 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 84 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 34 optimal weight: 0.0370 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.182059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.144238 restraints weight = 31451.165| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.75 r_work: 0.3169 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10841 Z= 0.122 Angle : 0.490 6.207 14678 Z= 0.262 Chirality : 0.036 0.140 1635 Planarity : 0.004 0.115 1826 Dihedral : 7.502 63.833 1515 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.75 % Favored : 93.94 % Rotamer: Outliers : 0.52 % Allowed : 8.87 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.24), residues: 1288 helix: 0.80 (0.21), residues: 707 sheet: -1.45 (0.45), residues: 120 loop : -1.95 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 944 TYR 0.044 0.001 TYR A1026 PHE 0.016 0.001 PHE A 585 TRP 0.007 0.001 TRP A 473 HIS 0.011 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (10841) covalent geometry : angle 0.49032 / 0.26 (14678) hydrogen bonds : bond 0.03652 / 2.40 ( 498) hydrogen bonds : angle 4.31751 / 3.05 ( 1467) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4933.95 seconds wall clock time: 84 minutes 27.43 seconds (5067.43 seconds total)