Starting phenix.real_space_refine on Sun Aug 24 16:46:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p1m_17354/08_2025/8p1m_17354_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p1m_17354/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8p1m_17354/08_2025/8p1m_17354_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p1m_17354/08_2025/8p1m_17354_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p1m_17354/08_2025/8p1m_17354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p1m_17354/08_2025/8p1m_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-2.0-5787/lib/python3.9/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: 3.48, per 1000 atoms: 0.16 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: 2.35 Conformation dependent library (CDL) restraints added in 724.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 239 through 251 removed outlier: 3.784A pdb=" N LEU A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 282 removed outlier: 3.672A pdb=" N CYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 removed outlier: 3.756A pdb=" N GLN A 311 " --> pdb=" O THR A 307 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 409 through 427 removed outlier: 3.857A pdb=" N GLN A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 470 through 489 removed outlier: 3.517A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N HIS A 477 " --> pdb=" O TRP A 473 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 592 removed outlier: 3.502A pdb=" N GLU A 590 " --> pdb=" O GLN A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 614 removed outlier: 3.771A pdb=" N ARG A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 603 " --> pdb=" O TYR A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 634 removed outlier: 3.905A pdb=" N CYS A 620 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG A 627 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR A 628 " --> pdb=" O ASP A 624 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 639 through 648 Processing helix chain 'A' and resid 656 through 675 removed outlier: 3.799A pdb=" N GLN A 673 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 726 removed outlier: 3.993A pdb=" N LEU A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 758 removed outlier: 3.606A pdb=" N GLU A 737 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 744 " --> pdb=" O LYS A 740 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 765 removed outlier: 3.583A pdb=" N VAL A 764 " --> pdb=" O GLY A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 775 removed outlier: 3.648A pdb=" N ALA A 775 " --> pdb=" O TRP A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 798 Processing helix chain 'A' and resid 804 through 815 Processing helix chain 'A' and resid 848 through 859 Processing helix chain 'A' and resid 866 through 873 removed outlier: 3.720A pdb=" N GLU A 871 " --> pdb=" O LYS A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 917 removed outlier: 3.706A pdb=" N ALA A 914 " --> pdb=" O ASP A 910 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 915 " --> pdb=" O TYR A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 947 removed outlier: 3.745A pdb=" N GLY A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 992 removed outlier: 3.997A pdb=" N ARG A 987 " --> pdb=" O ALA A 983 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET A 991 " --> pdb=" O ARG A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1020 through 1028 Processing helix chain 'A' and resid 1034 through 1042 removed outlier: 3.523A pdb=" N GLN A1039 " --> pdb=" O PRO A1035 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE A1040 " --> pdb=" O HIS A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1084 Processing helix chain 'A' and resid 1113 through 1127 Processing helix chain 'A' and resid 1128 through 1134 removed outlier: 3.609A pdb=" N TRP A1131 " --> pdb=" O HIS A1128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A1132 " --> pdb=" O LEU A1129 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A1133 " --> pdb=" O HIS A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1152 removed outlier: 3.945A pdb=" N SER A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A1142 " --> pdb=" O MET A1138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A1143 " --> pdb=" O TRP A1139 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1175 removed outlier: 3.711A pdb=" N THR A1174 " --> pdb=" O GLU A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1190 removed outlier: 3.871A pdb=" N ILE A1188 " --> pdb=" O PRO A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1218 removed outlier: 3.837A pdb=" N ALA A1207 " --> pdb=" O ASP A1203 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A1209 " --> pdb=" O LEU A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1241 removed outlier: 3.502A pdb=" N ALA A1228 " --> pdb=" O VAL A1224 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A1229 " --> pdb=" O ALA A1225 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A1230 " --> pdb=" O GLN A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1254 removed outlier: 3.909A pdb=" N TYR A1253 " --> pdb=" O HIS A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1261 removed outlier: 3.526A pdb=" N THR A1261 " --> pdb=" O HIS A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1266 Processing helix chain 'A' and resid 1272 through 1279 Processing helix chain 'A' and resid 1282 through 1299 removed outlier: 3.832A pdb=" N LYS A1286 " --> pdb=" O GLY A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1304 No H-bonds generated for 'chain 'A' and resid 1302 through 1304' Processing helix chain 'A' and resid 1305 through 1319 Processing helix chain 'A' and resid 1356 through 1365 removed outlier: 3.620A pdb=" N SER A1362 " --> pdb=" O LEU A1358 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A1363 " --> pdb=" O GLU A1359 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1370 Processing helix chain 'A' and resid 1375 through 1388 removed outlier: 3.740A pdb=" N ILE A1381 " --> pdb=" O ASP A1377 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR A1382 " --> pdb=" O ASN A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1396 Processing helix chain 'A' and resid 1400 through 1412 removed outlier: 4.025A pdb=" N GLN A1409 " --> pdb=" O ARG A1405 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA A1410 " --> pdb=" O PHE A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1439 removed outlier: 3.502A pdb=" N LEU A1430 " --> pdb=" O PHE A1426 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A1431 " --> pdb=" O ARG A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1454 Processing helix chain 'A' and resid 1502 through 1511 Processing helix chain 'A' and resid 1514 through 1525 Processing helix chain 'A' and resid 1530 through 1546 removed outlier: 3.839A pdb=" N ARG A1544 " --> pdb=" O ASP A1540 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A1545 " --> pdb=" O GLY A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1568 removed outlier: 4.079A pdb=" N ILE A1559 " --> pdb=" O VAL A1555 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A1560 " --> pdb=" O MET A1556 " (cutoff:3.500A) Proline residue: A1561 - end of helix Processing helix chain 'A' and resid 1581 through 1592 Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261 removed outlier: 4.376A pdb=" N THR A1163 " --> pdb=" O SER A 970 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A1100 " --> pdb=" O ALA A 971 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 503 removed outlier: 3.688A pdb=" N VAL A 508 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 531 " --> pdb=" O GLY A 555 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 499 through 503 removed outlier: 3.688A pdb=" N VAL A 508 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 527 " --> pdb=" O MET A 560 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AA5, first strand: chain 'A' and resid 832 through 837 removed outlier: 5.625A pdb=" N SER A 844 " --> pdb=" O GLY A 835 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 892 through 897 removed outlier: 4.322A pdb=" N ARG A 892 " --> pdb=" O LYS A 884 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA A 877 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE A 881 " --> pdb=" O PHE A1018 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 949 through 953 Processing sheet with id=AA8, first strand: chain 'A' and resid 1486 through 1491 removed outlier: 3.888A pdb=" N ARG A1570 " --> pdb=" O PHE A1490 " (cutoff:3.500A) 507 hydrogen bonds defined for protein. 1467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.58 Time building geometry restraints manager: 3.16 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: 2.620 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: 0.110 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 22.450 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: 0.020 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.070 ------------------------------------------------------------------------------- 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 : 8.04 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 aren 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 covalent geometry : bond 0.00343 (10841) covalent geometry : angle 0.54046 (14678) hydrogen bonds : bond 0.16271 ( 498) hydrogen bonds : angle 6.20072 ( 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 : 0.393 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: 0.2976 time to fit residues: 55.9665 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 : 0.578 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3897 r_free = 0.3897 target = 0.172381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133928 restraints weight = 31839.794| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.75 r_work: 0.3175 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.0700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 10841 Z= 0.139 Angle : 0.516 7.275 14678 Z= 0.281 Chirality : 0.037 0.139 1635 Planarity : 0.004 0.126 1826 Dihedral : 8.071 63.779 1515 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.90 % Favored : 93.79 % Rotamer: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.24), residues: 1288 helix: 0.59 (0.20), residues: 697 sheet: -1.28 (0.46), residues: 116 loop : -1.93 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1418 TYR 0.015 0.001 TYR A1026 PHE 0.015 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 covalent geometry : bond 0.00320 (10841) covalent geometry : angle 0.51648 (14678) hydrogen bonds : bond 0.04738 ( 498) hydrogen bonds : angle 4.86258 ( 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 133 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7765 (mp) cc_final: 0.7366 (tp) REVERT: A 563 ASP cc_start: 0.8668 (p0) cc_final: 0.8326 (p0) REVERT: A 929 GLU cc_start: 0.7172 (pp20) cc_final: 0.6383 (pp20) REVERT: A 1357 PHE cc_start: 0.7955 (t80) cc_final: 0.7341 (t80) REVERT: A 1408 MET cc_start: 0.6737 (tpt) cc_final: 0.6456 (tpt) outliers start: 2 outliers final: 1 residues processed: 131 average time/residue: 0.2787 time to fit residues: 50.7415 Evaluate side-chains 126 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1315 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 66 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 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: 1.6988 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.175362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.139829 restraints weight = 31906.060| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.72 r_work: 0.3135 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10841 Z= 0.209 Angle : 0.546 7.900 14678 Z= 0.295 Chirality : 0.038 0.149 1635 Planarity : 0.004 0.128 1826 Dihedral : 8.048 63.816 1515 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.91 % Favored : 92.78 % Rotamer: Outliers : 0.26 % Allowed : 5.91 % Favored : 93.83 % 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 aren not related in a simple way. whole: -0.99 (0.23), residues: 1288 helix: 0.41 (0.20), residues: 701 sheet: -1.40 (0.46), residues: 116 loop : -2.06 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1418 TYR 0.021 0.002 TYR A1026 PHE 0.017 0.002 PHE A 585 TRP 0.012 0.001 TRP A 473 HIS 0.014 0.001 HIS A 732 Details of bonding type rmsd covalent geometry : bond 0.00500 (10841) covalent geometry : angle 0.54610 (14678) hydrogen bonds : bond 0.04662 ( 498) hydrogen bonds : angle 4.78472 ( 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 129 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7793 (mp) cc_final: 0.7393 (tp) REVERT: A 929 GLU cc_start: 0.7168 (pp20) cc_final: 0.6267 (pp20) REVERT: A 1408 MET cc_start: 0.6646 (tpt) cc_final: 0.6397 (tpt) outliers start: 3 outliers final: 2 residues processed: 127 average time/residue: 0.2643 time to fit residues: 46.4617 Evaluate side-chains 124 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 1046 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 126 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3948 r_free = 0.3948 target = 0.176562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138908 restraints weight = 31827.818| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.73 r_work: 0.3156 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10841 Z= 0.158 Angle : 0.513 7.201 14678 Z= 0.275 Chirality : 0.037 0.146 1635 Planarity : 0.004 0.125 1826 Dihedral : 7.854 63.828 1515 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.29 % Favored : 93.40 % Rotamer: Outliers : 0.61 % Allowed : 7.48 % Favored : 91.91 % 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 aren not related in a simple way. whole: -0.85 (0.24), residues: 1288 helix: 0.54 (0.20), residues: 704 sheet: -1.44 (0.45), residues: 116 loop : -2.02 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 944 TYR 0.018 0.001 TYR A1026 PHE 0.016 0.001 PHE A 585 TRP 0.009 0.001 TRP A 473 HIS 0.014 0.001 HIS A 732 Details of bonding type rmsd covalent geometry : bond 0.00378 (10841) covalent geometry : angle 0.51288 (14678) hydrogen bonds : bond 0.04104 ( 498) hydrogen bonds : angle 4.56381 ( 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 139 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7834 (mp) cc_final: 0.7434 (tp) REVERT: A 929 GLU cc_start: 0.7242 (pp20) cc_final: 0.6305 (pp20) REVERT: A 1408 MET cc_start: 0.6637 (tpt) cc_final: 0.6369 (tpt) outliers start: 7 outliers final: 4 residues processed: 136 average time/residue: 0.2371 time to fit residues: 44.5718 Evaluate side-chains 134 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 1596 VAL 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: 1.9990 chunk 126 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.181601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.142934 restraints weight = 31580.464| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.81 r_work: 0.3152 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1232 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= 0.140 Angle : 0.496 6.885 14678 Z= 0.266 Chirality : 0.036 0.140 1635 Planarity : 0.004 0.122 1826 Dihedral : 7.724 63.831 1515 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.37 % Favored : 93.32 % Rotamer: Outliers : 0.52 % Allowed : 8.26 % Favored : 91.22 % 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 aren not related in a simple way. whole: -0.71 (0.24), residues: 1288 helix: 0.69 (0.20), residues: 707 sheet: -1.43 (0.45), residues: 116 loop : -2.00 (0.27), residues: 465 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 0.009 0.001 TRP A 473 HIS 0.013 0.001 HIS A 732 Details of bonding type rmsd covalent geometry : bond 0.00333 (10841) covalent geometry : angle 0.49621 (14678) hydrogen bonds : bond 0.03837 ( 498) hydrogen bonds : angle 4.40880 ( 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 135 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7811 (mp) cc_final: 0.7402 (tp) REVERT: A 759 TYR cc_start: 0.6338 (m-80) cc_final: 0.6035 (m-80) REVERT: A 929 GLU cc_start: 0.7278 (pp20) cc_final: 0.6299 (pp20) REVERT: A 1408 MET cc_start: 0.6605 (tpt) cc_final: 0.6211 (tpt) outliers start: 6 outliers final: 4 residues processed: 131 average time/residue: 0.2294 time to fit residues: 41.0501 Evaluate side-chains 130 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 47 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 87 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.181065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.143168 restraints weight = 31661.393| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.75 r_work: 0.3154 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: 0.7502 moved from start: 0.1323 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= 0.152 Angle : 0.498 6.776 14678 Z= 0.268 Chirality : 0.037 0.141 1635 Planarity : 0.004 0.121 1826 Dihedral : 7.663 63.832 1515 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.44 % Favored : 93.25 % Rotamer: Outliers : 0.61 % Allowed : 8.70 % 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 aren not related in a simple way. whole: -0.70 (0.24), residues: 1288 helix: 0.71 (0.20), residues: 707 sheet: -1.53 (0.44), residues: 120 loop : -2.01 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1418 TYR 0.024 0.001 TYR A1026 PHE 0.015 0.001 PHE A 585 TRP 0.009 0.001 TRP A 473 HIS 0.013 0.001 HIS A 732 Details of bonding type rmsd covalent geometry : bond 0.00365 (10841) covalent geometry : angle 0.49817 (14678) hydrogen bonds : bond 0.03826 ( 498) hydrogen bonds : angle 4.38547 ( 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: 7 poor density : 124 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7759 (mp) cc_final: 0.7355 (tp) REVERT: A 759 TYR cc_start: 0.6447 (m-80) cc_final: 0.6151 (m-80) REVERT: A 929 GLU cc_start: 0.7342 (pp20) cc_final: 0.6378 (pp20) REVERT: A 1414 MET cc_start: 0.6022 (tpp) cc_final: 0.5752 (tpp) outliers start: 7 outliers final: 5 residues processed: 129 average time/residue: 0.2327 time to fit residues: 41.2962 Evaluate side-chains 125 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1596 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 35 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.179900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.141931 restraints weight = 31692.408| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.75 r_work: 0.3139 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1400 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 : 0.513 6.416 14678 Z= 0.276 Chirality : 0.037 0.142 1635 Planarity : 0.004 0.119 1826 Dihedral : 7.668 63.832 1515 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.68 % Favored : 93.01 % Rotamer: Outliers : 0.70 % Allowed : 9.74 % Favored : 89.57 % 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 aren not related in a simple way. whole: -0.75 (0.24), residues: 1288 helix: 0.68 (0.20), residues: 705 sheet: -1.52 (0.45), residues: 120 loop : -2.04 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 944 TYR 0.025 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 covalent geometry : bond 0.00424 (10841) covalent geometry : angle 0.51287 (14678) hydrogen bonds : bond 0.03966 ( 498) hydrogen bonds : angle 4.41496 ( 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 135 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7757 (mp) cc_final: 0.7337 (tp) REVERT: A 759 TYR cc_start: 0.6752 (m-80) cc_final: 0.6516 (m-80) REVERT: A 1408 MET cc_start: 0.6540 (tpt) cc_final: 0.6298 (tpt) REVERT: A 1414 MET cc_start: 0.6003 (tpp) cc_final: 0.5725 (tpp) outliers start: 8 outliers final: 6 residues processed: 131 average time/residue: 0.2414 time to fit residues: 44.0880 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 : 0.413 ------------------------------------------------------------------------------- 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 93 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.155808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.113872 restraints weight = 32584.971| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.92 r_work: 0.3101 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10841 Z= 0.188 Angle : 0.523 6.427 14678 Z= 0.282 Chirality : 0.038 0.144 1635 Planarity : 0.004 0.118 1826 Dihedral : 7.688 63.833 1515 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.83 % Favored : 92.86 % Rotamer: Outliers : 0.70 % Allowed : 9.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.24), residues: 1288 helix: 0.65 (0.20), residues: 704 sheet: -1.55 (0.45), residues: 120 loop : -2.04 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 944 TYR 0.027 0.001 TYR A1026 PHE 0.016 0.002 PHE A 585 TRP 0.010 0.001 TRP A 473 HIS 0.011 0.001 HIS A 732 Details of bonding type rmsd covalent geometry : bond 0.00454 (10841) covalent geometry : angle 0.52328 (14678) hydrogen bonds : bond 0.04059 ( 498) hydrogen bonds : angle 4.44878 ( 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 134 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7633 (mp) cc_final: 0.7225 (tp) REVERT: A 563 ASP cc_start: 0.8535 (p0) cc_final: 0.8306 (p0) REVERT: A 759 TYR cc_start: 0.7004 (m-80) cc_final: 0.6791 (m-80) REVERT: A 1396 MET cc_start: 0.7875 (mtp) cc_final: 0.7544 (mtp) REVERT: A 1414 MET cc_start: 0.5906 (tpp) cc_final: 0.5653 (tpp) outliers start: 8 outliers final: 8 residues processed: 131 average time/residue: 0.2893 time to fit residues: 52.5873 Evaluate side-chains 134 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 735 MET 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: 0.9990 chunk 91 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.177710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.140074 restraints weight = 31547.155| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.72 r_work: 0.3167 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10841 Z= 0.129 Angle : 0.488 6.493 14678 Z= 0.262 Chirality : 0.036 0.141 1635 Planarity : 0.004 0.114 1826 Dihedral : 7.504 63.832 1515 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.67 % Favored : 94.02 % Rotamer: Outliers : 0.70 % Allowed : 9.91 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.24), residues: 1288 helix: 0.84 (0.21), residues: 706 sheet: -1.43 (0.45), residues: 119 loop : -1.97 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1418 TYR 0.031 0.001 TYR A1026 PHE 0.016 0.001 PHE A 585 TRP 0.008 0.001 TRP A 473 HIS 0.010 0.001 HIS A 732 Details of bonding type rmsd covalent geometry : bond 0.00308 (10841) covalent geometry : angle 0.48775 (14678) hydrogen bonds : bond 0.03649 ( 498) hydrogen bonds : angle 4.27303 ( 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 140 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7755 (mp) cc_final: 0.7324 (tp) REVERT: A 563 ASP cc_start: 0.8518 (p0) cc_final: 0.8306 (p0) REVERT: A 759 TYR cc_start: 0.7082 (m-80) cc_final: 0.6871 (m-80) REVERT: A 1396 MET cc_start: 0.7861 (mtp) cc_final: 0.7527 (mtp) REVERT: A 1408 MET cc_start: 0.6520 (tpt) cc_final: 0.6186 (tpt) REVERT: A 1414 MET cc_start: 0.5904 (tpp) cc_final: 0.5656 (tpp) outliers start: 8 outliers final: 8 residues processed: 137 average time/residue: 0.2458 time to fit residues: 47.2241 Evaluate side-chains 137 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 735 MET 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: 3.9990 chunk 77 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.177326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.139924 restraints weight = 31522.478| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.70 r_work: 0.3164 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1549 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= 0.137 Angle : 0.494 8.520 14678 Z= 0.265 Chirality : 0.036 0.141 1635 Planarity : 0.004 0.113 1826 Dihedral : 7.460 63.834 1515 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.21 % Favored : 93.48 % Rotamer: Outliers : 0.61 % Allowed : 10.17 % Favored : 89.22 % 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 aren not related in a simple way. whole: -0.51 (0.24), residues: 1288 helix: 0.88 (0.21), residues: 706 sheet: -1.46 (0.44), residues: 120 loop : -1.94 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 944 TYR 0.043 0.001 TYR A1026 PHE 0.015 0.001 PHE A 585 TRP 0.008 0.001 TRP A 473 HIS 0.010 0.001 HIS A 732 Details of bonding type rmsd covalent geometry : bond 0.00328 (10841) covalent geometry : angle 0.49433 (14678) hydrogen bonds : bond 0.03651 ( 498) hydrogen bonds : angle 4.25625 ( 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 135 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.7762 (mp) cc_final: 0.7324 (tp) REVERT: A 563 ASP cc_start: 0.8526 (p0) cc_final: 0.8317 (p0) REVERT: A 759 TYR cc_start: 0.7144 (m-80) cc_final: 0.6943 (m-80) REVERT: A 1357 PHE cc_start: 0.7893 (t80) cc_final: 0.7440 (t80) REVERT: A 1396 MET cc_start: 0.7846 (mtp) cc_final: 0.7514 (mtp) REVERT: A 1408 MET cc_start: 0.6524 (tpt) cc_final: 0.6184 (tpt) REVERT: A 1414 MET cc_start: 0.5959 (tpp) cc_final: 0.5673 (tpp) outliers start: 7 outliers final: 7 residues processed: 133 average time/residue: 0.2135 time to fit residues: 40.0407 Evaluate side-chains 135 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 84 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 123 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.178420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.141218 restraints weight = 31407.787| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.70 r_work: 0.3182 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10841 Z= 0.117 Angle : 0.483 8.921 14678 Z= 0.259 Chirality : 0.036 0.136 1635 Planarity : 0.003 0.027 1826 Dihedral : 7.409 63.833 1515 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.67 % Favored : 94.02 % 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 : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.24), residues: 1288 helix: 0.98 (0.21), residues: 714 sheet: -1.21 (0.47), residues: 109 loop : -1.93 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 944 TYR 0.040 0.001 TYR A1026 PHE 0.015 0.001 PHE A 585 TRP 0.007 0.001 TRP A 473 HIS 0.009 0.001 HIS A 732 Details of bonding type rmsd covalent geometry : bond 0.00277 (10841) covalent geometry : angle 0.48272 (14678) hydrogen bonds : bond 0.03471 ( 498) hydrogen bonds : angle 4.17564 ( 1467) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4654.74 seconds wall clock time: 79 minutes 46.58 seconds (4786.58 seconds total)