Starting phenix.real_space_refine on Wed May 21 12:02:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p1m_17354/05_2025/8p1m_17354_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p1m_17354/05_2025/8p1m_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_17354/05_2025/8p1m_17354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p1m_17354/05_2025/8p1m_17354.map" model { file = "/net/cci-nas-00/data/ceres_data/8p1m_17354/05_2025/8p1m_17354_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p1m_17354/05_2025/8p1m_17354_trim.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.72, per 1000 atoms: 0.46 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: 5.39 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.89 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: 8.52 Time building geometry restraints manager: 6.49 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: 0.010 Normalize map: mean=0, sd=1: 1.700 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: 0.350 Extract box with map and model: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 45.560 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 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= 0.147 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 : 8.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.001 TRP A 498 HIS 0.011 0.001 HIS A 732 PHE 0.016 0.001 PHE A 585 TYR 0.016 0.001 TYR A1026 ARG 0.007 0.000 ARG A1418 Details of bonding type rmsd hydrogen bonds : bond 0.16271 ( 498) hydrogen bonds : angle 6.20072 ( 1467) covalent geometry : bond 0.00343 (10841) covalent geometry : angle 0.54046 (14678) *********************** 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 : 1.513 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: 0.6319 time to fit residues: 120.7709 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 : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.172158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.133952 restraints weight = 32065.405| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.74 r_work: 0.3132 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10841 Z= 0.216 Angle : 0.566 8.060 14678 Z= 0.308 Chirality : 0.039 0.149 1635 Planarity : 0.005 0.130 1826 Dihedral : 8.191 63.965 1515 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.99 % Favored : 92.70 % Rotamer: Outliers : 0.43 % Allowed : 5.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.23), residues: 1288 helix: 0.29 (0.20), residues: 697 sheet: -1.41 (0.46), residues: 116 loop : -2.04 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 473 HIS 0.016 0.001 HIS A 732 PHE 0.017 0.002 PHE A 585 TYR 0.016 0.002 TYR A1026 ARG 0.009 0.000 ARG A1418 Details of bonding type rmsd hydrogen bonds : bond 0.04885 ( 498) hydrogen bonds : angle 5.01639 ( 1467) covalent geometry : bond 0.00515 (10841) covalent geometry : angle 0.56608 (14678) *********************** 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: 5 poor density : 126 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.7865 (tpp) cc_final: 0.7638 (tpp) REVERT: A 388 LEU cc_start: 0.7791 (mp) cc_final: 0.7382 (tp) REVERT: A 389 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8567 (mp) REVERT: A 929 GLU cc_start: 0.7206 (pp20) cc_final: 0.6360 (pp20) REVERT: A 1408 MET cc_start: 0.6739 (tpt) cc_final: 0.6475 (tpt) outliers start: 5 outliers final: 3 residues processed: 127 average time/residue: 0.5944 time to fit residues: 104.1644 Evaluate side-chains 125 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 389 LEU 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 57 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.157967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.116292 restraints weight = 32352.741| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.92 r_work: 0.3136 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10841 Z= 0.136 Angle : 0.499 7.363 14678 Z= 0.269 Chirality : 0.037 0.142 1635 Planarity : 0.004 0.126 1826 Dihedral : 7.901 63.828 1515 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.13 % Favored : 93.56 % Rotamer: Outliers : 0.26 % Allowed : 6.09 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.24), residues: 1288 helix: 0.55 (0.20), residues: 701 sheet: -1.37 (0.46), residues: 116 loop : -2.00 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 473 HIS 0.013 0.001 HIS A 732 PHE 0.015 0.001 PHE A 585 TYR 0.010 0.001 TYR A 869 ARG 0.004 0.000 ARG A1418 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 498) hydrogen bonds : angle 4.61005 ( 1467) covalent geometry : bond 0.00321 (10841) covalent geometry : angle 0.49949 (14678) *********************** 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 133 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.7789 (tpp) cc_final: 0.7573 (tpp) REVERT: A 388 LEU cc_start: 0.7711 (mp) cc_final: 0.7336 (tp) REVERT: A 389 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8453 (mp) REVERT: A 929 GLU cc_start: 0.7171 (pp20) cc_final: 0.6270 (pp20) REVERT: A 1408 MET cc_start: 0.6650 (tpt) cc_final: 0.6399 (tpt) outliers start: 3 outliers final: 1 residues processed: 131 average time/residue: 0.5649 time to fit residues: 102.8638 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 : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 389 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 122 optimal weight: 0.0060 chunk 44 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.178478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.140611 restraints weight = 31814.406| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.74 r_work: 0.3167 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10841 Z= 0.131 Angle : 0.490 6.734 14678 Z= 0.264 Chirality : 0.036 0.140 1635 Planarity : 0.004 0.122 1826 Dihedral : 7.755 63.830 1515 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.44 % Favored : 93.25 % Rotamer: Outliers : 0.43 % Allowed : 7.22 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.24), residues: 1288 helix: 0.71 (0.20), residues: 702 sheet: -1.44 (0.45), residues: 118 loop : -1.97 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 473 HIS 0.011 0.001 HIS A 732 PHE 0.015 0.001 PHE A 585 TYR 0.011 0.001 TYR A1026 ARG 0.007 0.000 ARG A 944 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 498) hydrogen bonds : angle 4.45688 ( 1467) covalent geometry : bond 0.00311 (10841) covalent geometry : angle 0.49042 (14678) *********************** 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 133 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7734 (mp) cc_final: 0.7353 (tp) REVERT: A 389 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8450 (mp) REVERT: A 929 GLU cc_start: 0.7184 (pp20) cc_final: 0.6237 (pp20) REVERT: A 1408 MET cc_start: 0.6546 (tpt) cc_final: 0.6164 (tpt) outliers start: 5 outliers final: 2 residues processed: 131 average time/residue: 0.5758 time to fit residues: 103.8450 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 : 1.445 ------------------------------------------------------------------------------- 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 389 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 36 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.176357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.138560 restraints weight = 31782.649| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.71 r_work: 0.3148 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 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 : 0.004 0.061 10841 Z= 0.176 Angle : 0.515 6.973 14678 Z= 0.277 Chirality : 0.037 0.141 1635 Planarity : 0.004 0.122 1826 Dihedral : 7.773 63.831 1515 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.99 % Favored : 92.70 % Rotamer: Outliers : 0.35 % Allowed : 8.61 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.24), residues: 1288 helix: 0.61 (0.20), residues: 707 sheet: -1.43 (0.45), residues: 116 loop : -2.06 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 473 HIS 0.011 0.001 HIS A 732 PHE 0.016 0.001 PHE A 585 TYR 0.013 0.001 TYR A 759 ARG 0.004 0.000 ARG A1418 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 498) hydrogen bonds : angle 4.49480 ( 1467) covalent geometry : bond 0.00422 (10841) covalent geometry : angle 0.51460 (14678) *********************** 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 : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7752 (mp) cc_final: 0.7349 (tp) REVERT: A 929 GLU cc_start: 0.7294 (pp20) cc_final: 0.6298 (pp20) REVERT: A 1408 MET cc_start: 0.6621 (tpt) cc_final: 0.6211 (tpt) outliers start: 4 outliers final: 3 residues processed: 129 average time/residue: 0.5711 time to fit residues: 102.5180 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 : 1.516 ------------------------------------------------------------------------------- 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 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 106 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.175956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.138217 restraints weight = 31470.028| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.72 r_work: 0.3143 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1291 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 : 0.518 6.957 14678 Z= 0.279 Chirality : 0.037 0.142 1635 Planarity : 0.004 0.121 1826 Dihedral : 7.733 63.832 1515 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.75 % Favored : 92.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.24), residues: 1288 helix: 0.62 (0.20), residues: 705 sheet: -1.50 (0.44), residues: 120 loop : -2.05 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 473 HIS 0.011 0.001 HIS A 732 PHE 0.016 0.001 PHE A 585 TYR 0.022 0.001 TYR A 759 ARG 0.004 0.000 ARG A 944 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 498) hydrogen bonds : angle 4.47290 ( 1467) covalent geometry : bond 0.00424 (10841) covalent geometry : angle 0.51837 (14678) *********************** 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 134 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ILE cc_start: 0.7363 (pt) cc_final: 0.7111 (tt) REVERT: A 388 LEU cc_start: 0.7725 (mp) cc_final: 0.7310 (tp) REVERT: A 929 GLU cc_start: 0.7370 (pp20) cc_final: 0.6392 (pp20) outliers start: 6 outliers final: 6 residues processed: 132 average time/residue: 0.5772 time to fit residues: 106.1012 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 : 1.554 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 93 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.182304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.144285 restraints weight = 31557.013| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.76 r_work: 0.3165 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10841 Z= 0.121 Angle : 0.486 6.059 14678 Z= 0.260 Chirality : 0.036 0.140 1635 Planarity : 0.004 0.117 1826 Dihedral : 7.560 63.831 1515 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.13 % Favored : 93.56 % Rotamer: Outliers : 0.61 % Allowed : 9.57 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.24), residues: 1288 helix: 0.83 (0.21), residues: 706 sheet: -1.45 (0.45), residues: 120 loop : -1.94 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 473 HIS 0.010 0.001 HIS A 732 PHE 0.015 0.001 PHE A 585 TYR 0.018 0.001 TYR A1026 ARG 0.005 0.000 ARG A1418 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 498) hydrogen bonds : angle 4.28903 ( 1467) covalent geometry : bond 0.00289 (10841) covalent geometry : angle 0.48572 (14678) *********************** 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 133 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 ILE cc_start: 0.7342 (pt) cc_final: 0.7070 (tt) REVERT: A 388 LEU cc_start: 0.7698 (mp) cc_final: 0.7293 (tp) REVERT: A 563 ASP cc_start: 0.8468 (p0) cc_final: 0.8251 (p0) REVERT: A 929 GLU cc_start: 0.7370 (pp20) cc_final: 0.6399 (pp20) REVERT: A 1408 MET cc_start: 0.6480 (tpt) cc_final: 0.6260 (tpt) outliers start: 7 outliers final: 6 residues processed: 130 average time/residue: 0.5649 time to fit residues: 102.4524 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 : 1.665 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.173781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.136001 restraints weight = 31821.633| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.72 r_work: 0.3115 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10841 Z= 0.235 Angle : 0.556 6.642 14678 Z= 0.300 Chirality : 0.039 0.145 1635 Planarity : 0.005 0.119 1826 Dihedral : 7.781 63.834 1515 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.61 % Favored : 92.08 % Rotamer: Outliers : 0.78 % Allowed : 9.91 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.24), residues: 1288 helix: 0.49 (0.20), residues: 705 sheet: -1.53 (0.45), residues: 120 loop : -2.11 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 473 HIS 0.011 0.001 HIS A 732 PHE 0.017 0.002 PHE A 585 TYR 0.025 0.002 TYR A 759 ARG 0.005 0.000 ARG A 944 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 498) hydrogen bonds : angle 4.56592 ( 1467) covalent geometry : bond 0.00567 (10841) covalent geometry : angle 0.55575 (14678) *********************** 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 135 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 1.489 Fit side-chains revert: symmetry clash REVERT: A 236 ILE cc_start: 0.7371 (pt) cc_final: 0.7063 (tt) REVERT: A 388 LEU cc_start: 0.7764 (mp) cc_final: 0.7326 (tp) outliers start: 9 outliers final: 7 residues processed: 132 average time/residue: 0.5666 time to fit residues: 104.6155 Evaluate side-chains 130 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 110 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.181377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.143509 restraints weight = 31660.975| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.75 r_work: 0.3155 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10841 Z= 0.125 Angle : 0.497 6.207 14678 Z= 0.266 Chirality : 0.036 0.140 1635 Planarity : 0.004 0.115 1826 Dihedral : 7.564 63.831 1515 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.98 % Favored : 93.71 % Rotamer: Outliers : 0.52 % Allowed : 10.17 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.24), residues: 1288 helix: 0.73 (0.20), residues: 707 sheet: -1.38 (0.45), residues: 119 loop : -2.01 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 473 HIS 0.010 0.001 HIS A 732 PHE 0.016 0.001 PHE A 585 TYR 0.017 0.001 TYR A1026 ARG 0.005 0.000 ARG A 944 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 498) hydrogen bonds : angle 4.33146 ( 1467) covalent geometry : bond 0.00299 (10841) covalent geometry : angle 0.49673 (14678) *********************** 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 133 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7697 (mp) cc_final: 0.7269 (tp) REVERT: A 563 ASP cc_start: 0.8508 (p0) cc_final: 0.8278 (p0) REVERT: A 1408 MET cc_start: 0.6588 (tpt) cc_final: 0.6229 (tpt) outliers start: 6 outliers final: 6 residues processed: 131 average time/residue: 0.5604 time to fit residues: 101.2098 Evaluate side-chains 133 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 THR 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 5 optimal weight: 2.9990 chunk 121 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 124 optimal weight: 0.0980 chunk 25 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.179239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.141859 restraints weight = 31467.207| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.71 r_work: 0.3187 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 10841 Z= 0.103 Angle : 0.474 5.788 14678 Z= 0.253 Chirality : 0.036 0.141 1635 Planarity : 0.004 0.111 1826 Dihedral : 7.349 63.833 1515 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.82 % Favored : 93.87 % Rotamer: Outliers : 0.35 % Allowed : 10.00 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.24), residues: 1288 helix: 0.97 (0.21), residues: 713 sheet: -1.38 (0.44), residues: 121 loop : -1.92 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 976 HIS 0.009 0.001 HIS A 732 PHE 0.015 0.001 PHE A 585 TYR 0.016 0.001 TYR A1026 ARG 0.005 0.000 ARG A 944 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 498) hydrogen bonds : angle 4.17801 ( 1467) covalent geometry : bond 0.00243 (10841) covalent geometry : angle 0.47385 (14678) ********************** 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 133 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 1.727 Fit side-chains revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7738 (mp) cc_final: 0.7301 (tp) REVERT: A 563 ASP cc_start: 0.8472 (p0) cc_final: 0.8264 (p0) REVERT: A 1408 MET cc_start: 0.6619 (tpt) cc_final: 0.6258 (tpt) outliers start: 4 outliers final: 2 residues processed: 131 average time/residue: 0.5893 time to fit residues: 108.0647 Evaluate side-chains 130 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 1046 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 128 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.181110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.143809 restraints weight = 31707.307| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.72 r_work: 0.3162 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10841 Z= 0.143 Angle : 0.493 5.900 14678 Z= 0.265 Chirality : 0.036 0.135 1635 Planarity : 0.003 0.026 1826 Dihedral : 7.436 63.833 1515 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.29 % Favored : 93.40 % Rotamer: Outliers : 0.43 % Allowed : 10.09 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.24), residues: 1288 helix: 0.93 (0.20), residues: 711 sheet: -1.54 (0.43), residues: 122 loop : -1.86 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 473 HIS 0.010 0.001 HIS A 732 PHE 0.015 0.001 PHE A 585 TYR 0.032 0.001 TYR A1026 ARG 0.005 0.000 ARG A 944 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 498) hydrogen bonds : angle 4.24882 ( 1467) covalent geometry : bond 0.00342 (10841) covalent geometry : angle 0.49332 (14678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9988.03 seconds wall clock time: 171 minutes 59.21 seconds (10319.21 seconds total)