Starting phenix.real_space_refine on Sat Jul 4 14:10:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p1m_17354/07_2026/8p1m_17354_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p1m_17354/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8p1m_17354/07_2026/8p1m_17354_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p1m_17354/07_2026/8p1m_17354_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p1m_17354/07_2026/8p1m_17354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p1m_17354/07_2026/8p1m_17354.map" } 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-dev-6108/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: 3.03, 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: 1.71 Conformation dependent library (CDL) restraints added in 539.8 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: 0.40 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: 4.62 Time building geometry restraints manager: 2.30 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: 37383 1.29 - 2.59: 1124 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=" 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 angle pdb=" N GLN A 592 " pdb=" CA GLN A 592 " pdb=" C GLN A 592 " ideal model delta sigma weight residual 114.56 110.68 3.88 1.27e+00 6.20e-01 9.34e+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: 1451 0.057 - 0.115: 162 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: 2.010 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: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.400 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.300 ------------------------------------------------------------------------------- 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 : 0.540 6.474 14678 Z= 0.307 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 0.00343 / 0.15 (10841) covalent geometry : angle 0.54046 / 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 : 0.545 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: 0.2264 time to fit residues: 43.5937 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 : 0.325 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.175411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137480 restraints weight = 31609.616| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.74 r_work: 0.3177 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.0626 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 : 0.532 7.731 14678 Z= 0.291 Chirality : 0.037 0.136 1635 Planarity : 0.004 0.129 1826 Dihedral : 8.189 63.897 1515 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.29 % Favored : 93.40 % Rotamer: Outliers : 0.35 % Allowed : 3.91 % Favored : 95.74 % 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: 0.54 (0.20), residues: 697 sheet: -1.41 (0.45), residues: 118 loop : -1.96 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1418 TYR 0.017 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 0.53203 / 0.29 (14678) hydrogen bonds : bond 0.05057 / 3.33 ( 498) hydrogen bonds : angle 4.98287 / 3.51 ( 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 132 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7766 (mp) cc_final: 0.7351 (tp) REVERT: A 563 ASP cc_start: 0.8667 (p0) cc_final: 0.8350 (p0) REVERT: A 929 GLU cc_start: 0.7166 (pp20) cc_final: 0.6346 (pp20) REVERT: A 1408 MET cc_start: 0.6664 (tpt) cc_final: 0.6406 (tpt) outliers start: 4 outliers final: 3 residues processed: 129 average time/residue: 0.2167 time to fit residues: 39.3598 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 : 0.357 ------------------------------------------------------------------------------- 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: 1.9990 chunk 118 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 125 optimal weight: 0.3980 chunk 27 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.173488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.135444 restraints weight = 31957.696| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.73 r_work: 0.3154 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10841 Z= 0.182 Angle : 0.526 8.153 14678 Z= 0.284 Chirality : 0.038 0.148 1635 Planarity : 0.004 0.130 1826 Dihedral : 8.067 63.832 1515 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.22 % Favored : 92.47 % 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: -0.89 (0.23), residues: 1288 helix: 0.50 (0.20), residues: 697 sheet: -1.39 (0.46), residues: 116 loop : -2.00 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1418 TYR 0.011 0.001 TYR A1026 PHE 0.015 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 0.00436 / 0.18 (10841) covalent geometry : angle 0.52598 / 0.28 (14678) hydrogen bonds : bond 0.04747 / 3.13 ( 498) hydrogen bonds : angle 4.80994 / 3.40 ( 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 130 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7725 (mp) cc_final: 0.7328 (tp) REVERT: A 563 ASP cc_start: 0.8721 (p0) cc_final: 0.8483 (p0) REVERT: A 929 GLU cc_start: 0.7137 (pp20) cc_final: 0.6302 (pp20) REVERT: A 1408 MET cc_start: 0.6660 (tpt) cc_final: 0.6410 (tpt) outliers start: 3 outliers final: 3 residues processed: 128 average time/residue: 0.2443 time to fit residues: 43.6915 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 : 0.531 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 126 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.176907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.141215 restraints weight = 31735.742| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.74 r_work: 0.3151 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10841 Z= 0.170 Angle : 0.518 8.027 14678 Z= 0.279 Chirality : 0.037 0.134 1635 Planarity : 0.004 0.129 1826 Dihedral : 7.978 63.817 1515 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.75 % Favored : 92.93 % Rotamer: Outliers : 0.26 % Allowed : 6.61 % Favored : 93.13 % 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: -0.92 (0.23), residues: 1288 helix: 0.51 (0.20), residues: 701 sheet: -1.49 (0.45), residues: 118 loop : -2.06 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1418 TYR 0.012 0.001 TYR A1026 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 0.00406 / 0.17 (10841) covalent geometry : angle 0.51757 / 0.28 (14678) hydrogen bonds : bond 0.04270 / 2.81 ( 498) hydrogen bonds : angle 4.67480 / 3.31 ( 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: 3 poor density : 124 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7810 (mp) cc_final: 0.7415 (tp) REVERT: A 929 GLU cc_start: 0.7156 (pp20) cc_final: 0.6236 (pp20) REVERT: A 1408 MET cc_start: 0.6634 (tpt) cc_final: 0.6390 (tpt) outliers start: 3 outliers final: 2 residues processed: 126 average time/residue: 0.2428 time to fit residues: 42.9116 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 : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 382 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 24 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.171182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.132473 restraints weight = 31853.361| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.76 r_work: 0.3157 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1072 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= 0.136 Angle : 0.501 7.491 14678 Z= 0.268 Chirality : 0.036 0.142 1635 Planarity : 0.004 0.126 1826 Dihedral : 7.854 63.830 1515 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.44 % Favored : 93.25 % Rotamer: Outliers : 0.35 % Allowed : 7.83 % Favored : 91.83 % 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: -0.75 (0.24), residues: 1288 helix: 0.66 (0.20), residues: 702 sheet: -1.48 (0.45), residues: 118 loop : -2.00 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1418 TYR 0.011 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 0.00322 / 0.14 (10841) covalent geometry : angle 0.50069 / 0.27 (14678) hydrogen bonds : bond 0.04036 / 2.65 ( 498) hydrogen bonds : angle 4.54211 / 3.21 ( 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 131 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7806 (mp) cc_final: 0.7419 (tp) REVERT: A 929 GLU cc_start: 0.7176 (pp20) cc_final: 0.6239 (pp20) REVERT: A 1408 MET cc_start: 0.6592 (tpt) cc_final: 0.6330 (tpt) outliers start: 4 outliers final: 2 residues processed: 129 average time/residue: 0.2280 time to fit residues: 41.2159 Evaluate side-chains 129 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE 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: 1.9990 chunk 127 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 123 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.180904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.142852 restraints weight = 31604.184| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.76 r_work: 0.3151 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1134 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= 0.171 Angle : 0.515 7.188 14678 Z= 0.276 Chirality : 0.037 0.141 1635 Planarity : 0.004 0.124 1826 Dihedral : 7.834 63.832 1515 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.99 % Favored : 92.70 % Rotamer: Outliers : 0.52 % Allowed : 8.00 % Favored : 91.48 % 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: -0.80 (0.24), residues: 1288 helix: 0.61 (0.20), residues: 704 sheet: -1.43 (0.45), residues: 116 loop : -2.04 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1418 TYR 0.017 0.001 TYR A1026 PHE 0.016 0.001 PHE A 585 TRP 0.010 0.001 TRP A 473 HIS 0.011 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (10841) covalent geometry : angle 0.51534 / 0.28 (14678) hydrogen bonds : bond 0.04073 / 2.68 ( 498) hydrogen bonds : angle 4.53954 / 3.21 ( 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 131 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7756 (mp) cc_final: 0.7368 (tp) REVERT: A 929 GLU cc_start: 0.7232 (pp20) cc_final: 0.6272 (pp20) REVERT: A 1408 MET cc_start: 0.6527 (tpt) cc_final: 0.6144 (tpt) outliers start: 6 outliers final: 5 residues processed: 128 average time/residue: 0.2505 time to fit residues: 45.0346 Evaluate side-chains 130 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 735 MET Chi-restraints excluded: chain A residue 1046 ASP 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: 0.5980 chunk 7 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.182787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.144845 restraints weight = 31476.878| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.75 r_work: 0.3174 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1197 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= 0.115 Angle : 0.489 6.699 14678 Z= 0.261 Chirality : 0.036 0.138 1635 Planarity : 0.004 0.121 1826 Dihedral : 7.709 63.831 1515 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.90 % Favored : 93.79 % Rotamer: Outliers : 0.52 % Allowed : 8.00 % Favored : 91.48 % 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: -0.58 (0.24), residues: 1288 helix: 0.81 (0.21), residues: 706 sheet: -1.52 (0.44), residues: 122 loop : -1.94 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 944 TYR 0.017 0.001 TYR A1026 PHE 0.015 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 0.00271 / 0.11 (10841) covalent geometry : angle 0.48872 / 0.26 (14678) hydrogen bonds : bond 0.03771 / 2.47 ( 498) hydrogen bonds : angle 4.38740 / 3.10 ( 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 132 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 ILE cc_start: 0.7348 (pt) cc_final: 0.7125 (tt) REVERT: A 388 LEU cc_start: 0.7742 (mp) cc_final: 0.7353 (tp) REVERT: A 563 ASP cc_start: 0.8646 (p0) cc_final: 0.8383 (p0) REVERT: A 929 GLU cc_start: 0.7224 (pp20) cc_final: 0.6252 (pp20) REVERT: A 1408 MET cc_start: 0.6488 (tpt) cc_final: 0.6106 (tpt) outliers start: 6 outliers final: 5 residues processed: 129 average time/residue: 0.2546 time to fit residues: 46.2622 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 : 0.627 ------------------------------------------------------------------------------- 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 735 MET Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1596 VAL 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: 9.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.180756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.142833 restraints weight = 31665.752| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.76 r_work: 0.3149 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1240 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= 0.175 Angle : 0.512 6.735 14678 Z= 0.274 Chirality : 0.037 0.139 1635 Planarity : 0.004 0.120 1826 Dihedral : 7.727 63.834 1515 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.83 % Favored : 92.86 % Rotamer: Outliers : 0.61 % Allowed : 8.52 % 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: -0.73 (0.24), residues: 1288 helix: 0.67 (0.20), residues: 707 sheet: -1.51 (0.44), residues: 120 loop : -2.00 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 944 TYR 0.020 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 0.00422 / 0.18 (10841) covalent geometry : angle 0.51183 / 0.27 (14678) hydrogen bonds : bond 0.03943 / 2.60 ( 498) hydrogen bonds : angle 4.44895 / 3.15 ( 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 132 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 ILE cc_start: 0.7357 (pt) cc_final: 0.7111 (tt) REVERT: A 388 LEU cc_start: 0.7756 (mp) cc_final: 0.7359 (tp) REVERT: A 929 GLU cc_start: 0.7280 (pp20) cc_final: 0.6274 (pp20) REVERT: A 1408 MET cc_start: 0.6535 (tpt) cc_final: 0.6149 (tpt) outliers start: 7 outliers final: 5 residues processed: 130 average time/residue: 0.2396 time to fit residues: 43.9679 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 : 0.463 ------------------------------------------------------------------------------- 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: 0.9980 chunk 91 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.182167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144275 restraints weight = 31548.931| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.75 r_work: 0.3168 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1292 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= 0.127 Angle : 0.493 7.414 14678 Z= 0.263 Chirality : 0.036 0.138 1635 Planarity : 0.004 0.118 1826 Dihedral : 7.648 63.833 1515 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.98 % Favored : 93.71 % Rotamer: Outliers : 0.52 % Allowed : 8.96 % Favored : 90.52 % 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: -0.56 (0.24), residues: 1288 helix: 0.82 (0.20), residues: 707 sheet: -1.47 (0.44), residues: 120 loop : -1.93 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 944 TYR 0.020 0.001 TYR A1026 PHE 0.015 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 0.00305 / 0.13 (10841) covalent geometry : angle 0.49346 / 0.26 (14678) hydrogen bonds : bond 0.03732 / 2.45 ( 498) hydrogen bonds : angle 4.33842 / 3.07 ( 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 132 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 ILE cc_start: 0.7341 (pt) cc_final: 0.7088 (tt) REVERT: A 388 LEU cc_start: 0.7750 (mp) cc_final: 0.7352 (tp) REVERT: A 929 GLU cc_start: 0.7271 (pp20) cc_final: 0.6259 (pp20) REVERT: A 1408 MET cc_start: 0.6528 (tpt) cc_final: 0.6143 (tpt) outliers start: 6 outliers final: 5 residues processed: 130 average time/residue: 0.2414 time to fit residues: 43.8194 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 : 0.451 ------------------------------------------------------------------------------- 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: 0.7980 chunk 77 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.177357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.139900 restraints weight = 31475.411| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.70 r_work: 0.3164 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1332 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= 0.145 Angle : 0.501 7.564 14678 Z= 0.267 Chirality : 0.036 0.140 1635 Planarity : 0.004 0.116 1826 Dihedral : 7.612 63.834 1515 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.37 % Favored : 93.32 % Rotamer: Outliers : 0.52 % Allowed : 8.78 % 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: -0.60 (0.24), residues: 1288 helix: 0.79 (0.20), residues: 707 sheet: -1.47 (0.44), 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 0.026 0.001 TYR A1026 PHE 0.015 0.001 PHE A 585 TRP 0.009 0.001 TRP A 473 HIS 0.011 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (10841) covalent geometry : angle 0.50051 / 0.27 (14678) hydrogen bonds : bond 0.03741 / 2.46 ( 498) hydrogen bonds : angle 4.35423 / 3.08 ( 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 128 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 ILE cc_start: 0.7309 (pt) cc_final: 0.7052 (tt) REVERT: A 388 LEU cc_start: 0.7763 (mp) cc_final: 0.7357 (tp) REVERT: A 929 GLU cc_start: 0.7284 (pp20) cc_final: 0.6270 (pp20) REVERT: A 1396 MET cc_start: 0.7722 (mtp) cc_final: 0.7459 (mtp) outliers start: 6 outliers final: 6 residues processed: 126 average time/residue: 0.2278 time to fit residues: 40.4362 Evaluate side-chains 128 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 431 ILE 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: 0.9980 chunk 78 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 34 optimal weight: 0.0050 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.182391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144183 restraints weight = 31424.916| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.78 r_work: 0.3167 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1383 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= 0.119 Angle : 0.483 5.783 14678 Z= 0.258 Chirality : 0.036 0.138 1635 Planarity : 0.004 0.114 1826 Dihedral : 7.520 63.832 1515 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.06 % Favored : 93.63 % Rotamer: Outliers : 0.43 % Allowed : 8.96 % 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: -0.44 (0.24), residues: 1288 helix: 0.93 (0.21), residues: 706 sheet: -1.40 (0.45), residues: 119 loop : -1.88 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 944 TYR 0.019 0.001 TYR A1026 PHE 0.015 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 0.00285 / 0.12 (10841) covalent geometry : angle 0.48254 / 0.26 (14678) hydrogen bonds : bond 0.03582 / 2.35 ( 498) hydrogen bonds : angle 4.26789 / 3.02 ( 1467) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4674.48 seconds wall clock time: 80 minutes 1.97 seconds (4801.97 seconds total)