Starting phenix.real_space_refine on Thu Jul 2 23:04:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ci5_16670/07_2026/8ci5_16670.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ci5_16670/07_2026/8ci5_16670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ci5_16670/07_2026/8ci5_16670.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ci5_16670/07_2026/8ci5_16670.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ci5_16670/07_2026/8ci5_16670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ci5_16670/07_2026/8ci5_16670.map" model { file = "/net/cci-nas-00/data/ceres_data/8ci5_16670/07_2026/8ci5_16670.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ci5_16670/07_2026/8ci5_16670.cif" } resolution = 3.2 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= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 49 5.16 5 C 6629 2.51 5 N 1738 2.21 5 O 1938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10365 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10128 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1258, 10124 Classifications: {'peptide': 1258} Link IDs: {'PTRANS': 41, 'TRANS': 1216} Chain breaks: 15 Conformer: "B" Number of residues, atoms: 1258, 10124 Classifications: {'peptide': 1258} Link IDs: {'PTRANS': 41, 'TRANS': 1216} Chain breaks: 15 bond proxies already assigned to first conformer: 10337 Chain: "C" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 237 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 8} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLY A1047 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A1047 " occ=0.50 Time building chain proxies: 3.85, per 1000 atoms: 0.37 Number of scatterers: 10365 At special positions: 0 Unit cell: (101.15, 88.4, 125.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 11 15.00 O 1938 8.00 N 1738 7.00 C 6629 6.00 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: 0.79 Conformation dependent library (CDL) restraints added in 812.6 milliseconds 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2388 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 12 sheets defined 57.1% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 239 through 252 removed outlier: 3.760A pdb=" N LEU A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 removed outlier: 3.961A pdb=" N VAL A 277 " --> pdb=" O ASN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 345 through 353 removed outlier: 3.821A pdb=" N ILE A 350 " --> pdb=" O ARG A 346 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 removed outlier: 4.031A pdb=" N LEU A 378 " --> pdb=" O LEU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 removed outlier: 3.694A pdb=" N LYS A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 426 Processing helix chain 'A' and resid 451 through 464 Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 471 through 491 removed outlier: 3.690A pdb=" N HIS A 475 " --> pdb=" O THR A 471 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP A 482 " --> pdb=" O HIS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 573 Processing helix chain 'A' and resid 573 through 594 Processing helix chain 'A' and resid 598 through 616 removed outlier: 3.681A pdb=" N GLN A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 635 removed outlier: 3.587A pdb=" N CYS A 621 " --> pdb=" O LYS A 617 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 623 " --> pdb=" O LYS A 619 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR A 629 " --> pdb=" O ASP A 625 " (cutoff:3.500A) Proline residue: A 632 - end of helix removed outlier: 3.611A pdb=" N THR A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 649 removed outlier: 3.667A pdb=" N PHE A 649 " --> pdb=" O ILE A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 675 removed outlier: 3.754A pdb=" N VAL A 659 " --> pdb=" O SER A 655 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 675 " --> pdb=" O SER A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 727 removed outlier: 4.347A pdb=" N LEU A 717 " --> pdb=" O HIS A 713 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 727 " --> pdb=" O THR A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 742 through 761 removed outlier: 4.583A pdb=" N THR A 746 " --> pdb=" O ILE A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 768 removed outlier: 3.523A pdb=" N MET A 765 " --> pdb=" O GLY A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 777 Processing helix chain 'A' and resid 787 through 803 Processing helix chain 'A' and resid 805 through 815 removed outlier: 3.579A pdb=" N MET A 814 " --> pdb=" O SER A 810 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 815 " --> pdb=" O SER A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 830 removed outlier: 3.923A pdb=" N SER A 830 " --> pdb=" O ARG A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 861 removed outlier: 3.567A pdb=" N ASN A 858 " --> pdb=" O ILE A 854 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG A 859 " --> pdb=" O ARG A 855 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLN A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 873 Processing helix chain 'A' and resid 899 through 918 Processing helix chain 'A' and resid 932 through 947 removed outlier: 3.661A pdb=" N ALA A 947 " --> pdb=" O ALA A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 992 removed outlier: 4.451A pdb=" N ARG A 988 " --> pdb=" O ALA A 984 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 992 " --> pdb=" O ARG A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1011 Processing helix chain 'A' and resid 1021 through 1030 removed outlier: 3.515A pdb=" N ASP A1029 " --> pdb=" O HIS A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1045 removed outlier: 3.611A pdb=" N ASP A1040 " --> pdb=" O GLU A1036 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A1045 " --> pdb=" O PHE A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1083 Processing helix chain 'A' and resid 1115 through 1127 removed outlier: 3.668A pdb=" N ALA A1127 " --> pdb=" O GLN A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1135 removed outlier: 3.642A pdb=" N ALA A1134 " --> pdb=" O HIS A1131 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A1135 " --> pdb=" O TRP A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1154 Processing helix chain 'A' and resid 1186 through 1192 removed outlier: 3.521A pdb=" N LEU A1190 " --> pdb=" O PHE A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1219 removed outlier: 3.654A pdb=" N ASP A1205 " --> pdb=" O GLY A1201 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS A1213 " --> pdb=" O ALA A1209 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A1219 " --> pdb=" O LYS A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1242 Processing helix chain 'A' and resid 1250 through 1254 Processing helix chain 'A' and resid 1283 through 1301 removed outlier: 3.905A pdb=" N LYS A1287 " --> pdb=" O GLY A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1303 through 1318 removed outlier: 3.617A pdb=" N LEU A1318 " --> pdb=" O PHE A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1366 Processing helix chain 'A' and resid 1367 through 1371 removed outlier: 3.707A pdb=" N ASP A1370 " --> pdb=" O PRO A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1376 through 1390 removed outlier: 3.534A pdb=" N LEU A1380 " --> pdb=" O GLY A1376 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1398 Processing helix chain 'A' and resid 1401 through 1408 removed outlier: 4.240A pdb=" N LEU A1405 " --> pdb=" O SER A1401 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG A1406 " --> pdb=" O PRO A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1440 Processing helix chain 'A' and resid 1449 through 1456 Processing helix chain 'A' and resid 1504 through 1513 removed outlier: 4.239A pdb=" N TYR A1512 " --> pdb=" O ILE A1508 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1525 Processing helix chain 'A' and resid 1531 through 1547 removed outlier: 4.108A pdb=" N GLN A1537 " --> pdb=" O SER A1533 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A1546 " --> pdb=" O GLY A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1553 through 1558 removed outlier: 4.200A pdb=" N LEU A1557 " --> pdb=" O LEU A1553 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS A1558 " --> pdb=" O PRO A1554 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1553 through 1558' Processing helix chain 'A' and resid 1560 through 1567 removed outlier: 3.534A pdb=" N LEU A1564 " --> pdb=" O ILE A1560 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA A1567 " --> pdb=" O LEU A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1582 through 1593 removed outlier: 3.774A pdb=" N SER A1588 " --> pdb=" O GLU A1584 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A1589 " --> pdb=" O SER A1585 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.700A pdb=" N THR A1164 " --> pdb=" O SER A 971 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A1105 " --> pdb=" O MET A 968 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA A1101 " --> pdb=" O ALA A 972 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A1106 " --> pdb=" O PHE A1091 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 283 through 284 removed outlier: 5.830A pdb=" N LYS A 283 " --> pdb=" O SER A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 298 removed outlier: 4.158A pdb=" N ILE A 536 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 500 through 504 removed outlier: 5.174A pdb=" N THR A 530 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 553 " --> pdb=" O ILE A 550 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 500 through 504 removed outlier: 3.570A pdb=" N ILE A 563 " --> pdb=" O ILE A 526 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AA7, first strand: chain 'A' and resid 896 through 898 removed outlier: 7.082A pdb=" N ALA A 880 " --> pdb=" O PHE A1019 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 952 through 954 Processing sheet with id=AA9, first strand: chain 'A' and resid 964 through 965 Processing sheet with id=AB1, first strand: chain 'A' and resid 1170 through 1172 Processing sheet with id=AB2, first strand: chain 'A' and resid 1418 through 1420 Processing sheet with id=AB3, first strand: chain 'A' and resid 1486 through 1491 508 hydrogen bonds defined for protein. 1443 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: 1.97 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2288 1.33 - 1.45: 2508 1.45 - 1.57: 5715 1.57 - 1.69: 22 1.69 - 1.81: 79 Bond restraints: 10612 Sorted by residual: bond pdb=" CA SER A1193 " pdb=" C SER A1193 " ideal model delta sigma weight residual 1.522 1.462 0.061 1.34e-02 5.57e+03 2.04e+01 bond pdb=" C ILE A1264 " pdb=" N PRO A1265 " ideal model delta sigma weight residual 1.337 1.366 -0.030 9.80e-03 1.04e+04 9.14e+00 bond pdb=" N GLN A1059 " pdb=" CA GLN A1059 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.03e+00 bond pdb=" C ALA A 845 " pdb=" N ALA A 846 " ideal model delta sigma weight residual 1.334 1.294 0.040 1.52e-02 4.33e+03 6.89e+00 bond pdb=" CA LEU A 464 " pdb=" C LEU A 464 " ideal model delta sigma weight residual 1.524 1.506 0.018 7.00e-03 2.04e+04 6.89e+00 ... (remaining 10607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 13734 2.56 - 5.13: 572 5.13 - 7.69: 66 7.69 - 10.26: 9 10.26 - 12.82: 5 Bond angle restraints: 14386 Sorted by residual: angle pdb=" CA PRO A1391 " pdb=" N PRO A1391 " pdb=" CD PRO A1391 " ideal model delta sigma weight residual 112.00 100.12 11.88 1.40e+00 5.10e-01 7.20e+01 angle pdb=" N VAL A1049 " pdb=" CA VAL A1049 " pdb=" C VAL A1049 " ideal model delta sigma weight residual 113.47 106.24 7.23 1.01e+00 9.80e-01 5.13e+01 angle pdb=" N VAL A 277 " pdb=" CA VAL A 277 " pdb=" C VAL A 277 " ideal model delta sigma weight residual 111.77 105.89 5.88 1.04e+00 9.25e-01 3.19e+01 angle pdb=" C SER A1531 " pdb=" N LEU A1532 " pdb=" CA LEU A1532 " ideal model delta sigma weight residual 120.44 126.63 -6.19 1.30e+00 5.92e-01 2.27e+01 angle pdb=" N VAL A1252 " pdb=" CA VAL A1252 " pdb=" C VAL A1252 " ideal model delta sigma weight residual 113.07 106.88 6.19 1.37e+00 5.33e-01 2.04e+01 ... (remaining 14381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.94: 6020 26.94 - 53.87: 258 53.87 - 80.81: 29 80.81 - 107.75: 6 107.75 - 134.68: 1 Dihedral angle restraints: 6314 sinusoidal: 2624 harmonic: 3690 Sorted by residual: dihedral pdb=" O4' U C 7 " pdb=" C1' U C 7 " pdb=" N1 U C 7 " pdb=" C2 U C 7 " ideal model delta sinusoidal sigma weight residual 200.00 65.32 134.68 1 1.50e+01 4.44e-03 7.27e+01 dihedral pdb=" CA SER A 926 " pdb=" C SER A 926 " pdb=" N TYR A 927 " pdb=" CA TYR A 927 " ideal model delta harmonic sigma weight residual -180.00 -150.12 -29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ARG A 893 " pdb=" C ARG A 893 " pdb=" N GLY A 894 " pdb=" CA GLY A 894 " ideal model delta harmonic sigma weight residual 180.00 -153.88 -26.12 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 6311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1262 0.078 - 0.157: 312 0.157 - 0.235: 33 0.235 - 0.314: 2 0.314 - 0.392: 2 Chirality restraints: 1611 Sorted by residual: chirality pdb=" CB VAL A1135 " pdb=" CA VAL A1135 " pdb=" CG1 VAL A1135 " pdb=" CG2 VAL A1135 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA PRO A1391 " pdb=" N PRO A1391 " pdb=" C PRO A1391 " pdb=" CB PRO A1391 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CB VAL A1394 " pdb=" CA VAL A1394 " pdb=" CG1 VAL A1394 " pdb=" CG2 VAL A1394 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 1608 not shown) Planarity restraints: 1772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A1292 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C GLN A1292 " -0.055 2.00e-02 2.50e+03 pdb=" O GLN A1292 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA A1293 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A1390 " -0.053 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO A1391 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A1391 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A1391 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1297 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.22e+00 pdb=" C TYR A1297 " 0.050 2.00e-02 2.50e+03 pdb=" O TYR A1297 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS A1298 " -0.017 2.00e-02 2.50e+03 ... (remaining 1769 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1227 2.73 - 3.27: 9735 3.27 - 3.82: 16550 3.82 - 4.36: 20800 4.36 - 4.90: 35442 Nonbonded interactions: 83754 Sorted by model distance: nonbonded pdb=" O ILE A 408 " pdb=" NE2 GLN A 414 " model vdw 2.190 3.120 nonbonded pdb=" OE2 GLU A 739 " pdb=" OG SER A1021 " model vdw 2.211 3.040 nonbonded pdb=" O GLU A1580 " pdb=" OG SER A1585 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR A 913 " pdb=" OG1 THR A 990 " model vdw 2.233 3.040 nonbonded pdb=" O LEU A1119 " pdb=" OG SER A1122 " model vdw 2.242 3.040 ... (remaining 83749 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=0.50 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: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.870 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 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 : 0.014 0.116 10612 Z= 0.586 Angle : 1.190 12.820 14386 Z= 0.665 Chirality : 0.067 0.392 1611 Planarity : 0.008 0.073 1772 Dihedral : 15.027 134.683 3926 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.32 % Favored : 91.11 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.88 (0.20), residues: 1229 helix: -2.14 (0.16), residues: 658 sheet: -2.93 (0.44), residues: 105 loop : -2.94 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.002 ARG A1239 TYR 0.039 0.004 TYR A 504 PHE 0.048 0.005 PHE A1437 TRP 0.037 0.004 TRP A1424 HIS 0.011 0.003 HIS A 733 Details of bonding type rmsd/Z covalent geometry : bond 0.01401 / 0.59 (10612) covalent geometry : angle 1.18965 / 0.67 (14386) hydrogen bonds : bond 0.17699 / 11.14 ( 498) hydrogen bonds : angle 6.88475 / 4.88 ( 1443) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.399 Fit side-chains REVERT: A 345 ASN cc_start: 0.7830 (t0) cc_final: 0.7597 (t0) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1164 time to fit residues: 19.1457 Evaluate side-chains 102 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 GLN A 478 HIS A 626 ASN A 935 ASN A1059 GLN A1379 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.124514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099838 restraints weight = 16227.975| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.76 r_work: 0.3099 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10612 Z= 0.133 Angle : 0.570 7.989 14386 Z= 0.306 Chirality : 0.041 0.163 1611 Planarity : 0.005 0.058 1772 Dihedral : 6.969 133.822 1488 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.19 % Rotamer: Outliers : 0.18 % Allowed : 3.78 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.22), residues: 1229 helix: -0.30 (0.19), residues: 658 sheet: -2.00 (0.48), residues: 105 loop : -2.30 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 918 TYR 0.015 0.001 TYR A 504 PHE 0.026 0.002 PHE A1186 TRP 0.019 0.002 TRP A 474 HIS 0.004 0.001 HIS A 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (10612) covalent geometry : angle 0.56992 / 0.31 (14386) hydrogen bonds : bond 0.05107 / 3.26 ( 498) hydrogen bonds : angle 4.79716 / 3.45 ( 1443) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.409 Fit side-chains REVERT: A 893 ARG cc_start: 0.6674 (ttt-90) cc_final: 0.6284 (tpp80) REVERT: A 1120 TYR cc_start: 0.7829 (t80) cc_final: 0.7454 (t80) REVERT: A 1239 ARG cc_start: 0.7852 (ptp-110) cc_final: 0.7635 (ttp80) outliers start: 2 outliers final: 1 residues processed: 126 average time/residue: 0.1255 time to fit residues: 21.5494 Evaluate side-chains 110 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1133 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 96 optimal weight: 0.0770 chunk 52 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1061 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.121776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.096786 restraints weight = 16431.756| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.77 r_work: 0.3039 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10612 Z= 0.194 Angle : 0.592 7.246 14386 Z= 0.313 Chirality : 0.043 0.166 1611 Planarity : 0.005 0.061 1772 Dihedral : 6.729 131.614 1488 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.46 % Favored : 94.45 % Rotamer: Outliers : 0.81 % Allowed : 5.94 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.23), residues: 1229 helix: 0.26 (0.20), residues: 660 sheet: -1.73 (0.49), residues: 105 loop : -2.08 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 469 TYR 0.014 0.002 TYR A1383 PHE 0.024 0.002 PHE A1186 TRP 0.016 0.002 TRP A 474 HIS 0.004 0.001 HIS A 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (10612) covalent geometry : angle 0.59242 / 0.31 (14386) hydrogen bonds : bond 0.05750 / 3.67 ( 498) hydrogen bonds : angle 4.67636 / 3.36 ( 1443) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.428 Fit side-chains REVERT: A 1120 TYR cc_start: 0.7837 (t80) cc_final: 0.7490 (t80) REVERT: A 1173 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5550 (pp) outliers start: 9 outliers final: 5 residues processed: 117 average time/residue: 0.1166 time to fit residues: 18.8333 Evaluate side-chains 115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1133 HIS Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1532 LEU Chi-restraints excluded: chain A residue 1539 MET Chi-restraints excluded: chain A residue 1570 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.0870 chunk 75 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.125843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.101484 restraints weight = 16364.800| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.75 r_work: 0.3113 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10612 Z= 0.121 Angle : 0.512 7.546 14386 Z= 0.268 Chirality : 0.040 0.170 1611 Planarity : 0.004 0.061 1772 Dihedral : 6.038 131.918 1488 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.51 % Favored : 96.41 % Rotamer: Outliers : 0.54 % Allowed : 8.54 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.23), residues: 1229 helix: 0.84 (0.20), residues: 661 sheet: -1.40 (0.50), residues: 105 loop : -1.88 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 888 TYR 0.013 0.001 TYR A 913 PHE 0.019 0.002 PHE A1186 TRP 0.016 0.001 TRP A 474 HIS 0.003 0.001 HIS A 743 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (10612) covalent geometry : angle 0.51168 / 0.27 (14386) hydrogen bonds : bond 0.04404 / 2.82 ( 498) hydrogen bonds : angle 4.33116 / 3.12 ( 1443) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.398 Fit side-chains REVERT: A 561 MET cc_start: 0.8330 (mmt) cc_final: 0.8096 (mmm) REVERT: A 927 TYR cc_start: 0.5773 (t80) cc_final: 0.5557 (t80) REVERT: A 1120 TYR cc_start: 0.7808 (t80) cc_final: 0.7445 (t80) REVERT: A 1451 PHE cc_start: 0.7302 (m-10) cc_final: 0.7092 (m-10) outliers start: 6 outliers final: 3 residues processed: 122 average time/residue: 0.1073 time to fit residues: 18.0023 Evaluate side-chains 113 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1133 HIS Chi-restraints excluded: chain A residue 1215 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 117 optimal weight: 0.9980 chunk 123 optimal weight: 0.0870 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 115 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.125907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101694 restraints weight = 16199.095| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.75 r_work: 0.3120 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10612 Z= 0.111 Angle : 0.496 9.153 14386 Z= 0.257 Chirality : 0.039 0.166 1611 Planarity : 0.004 0.061 1772 Dihedral : 5.812 131.964 1488 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 0.81 % Allowed : 8.99 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.24), residues: 1229 helix: 1.23 (0.20), residues: 657 sheet: -1.04 (0.50), residues: 99 loop : -1.65 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 893 TYR 0.012 0.001 TYR A1307 PHE 0.019 0.001 PHE A1186 TRP 0.014 0.001 TRP A 946 HIS 0.003 0.001 HIS A 743 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (10612) covalent geometry : angle 0.49603 / 0.26 (14386) hydrogen bonds : bond 0.04154 / 2.67 ( 498) hydrogen bonds : angle 4.16933 / 3.00 ( 1443) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.289 Fit side-chains REVERT: A 561 MET cc_start: 0.8276 (mmt) cc_final: 0.8017 (mmm) REVERT: A 1120 TYR cc_start: 0.7830 (t80) cc_final: 0.7476 (t80) REVERT: A 1173 LEU cc_start: 0.6027 (OUTLIER) cc_final: 0.5612 (pp) outliers start: 9 outliers final: 4 residues processed: 123 average time/residue: 0.1094 time to fit residues: 18.4015 Evaluate side-chains 118 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 1133 HIS Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1197 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.124626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.099624 restraints weight = 16355.535| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.78 r_work: 0.3095 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10612 Z= 0.126 Angle : 0.515 7.988 14386 Z= 0.267 Chirality : 0.040 0.172 1611 Planarity : 0.004 0.061 1772 Dihedral : 5.803 130.656 1488 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.08 % Favored : 95.84 % Rotamer: Outliers : 0.81 % Allowed : 9.89 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.24), residues: 1229 helix: 1.26 (0.20), residues: 661 sheet: -0.94 (0.51), residues: 99 loop : -1.52 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1301 TYR 0.023 0.001 TYR A 927 PHE 0.020 0.002 PHE A1186 TRP 0.014 0.001 TRP A 474 HIS 0.003 0.001 HIS A 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (10612) covalent geometry : angle 0.51490 / 0.27 (14386) hydrogen bonds : bond 0.04393 / 2.82 ( 498) hydrogen bonds : angle 4.19650 / 3.02 ( 1443) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 561 MET cc_start: 0.8359 (mmt) cc_final: 0.8090 (mmm) REVERT: A 893 ARG cc_start: 0.6544 (ttt-90) cc_final: 0.6301 (ttt-90) REVERT: A 1120 TYR cc_start: 0.7890 (t80) cc_final: 0.7547 (t80) REVERT: A 1173 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5633 (pp) outliers start: 9 outliers final: 7 residues processed: 123 average time/residue: 0.1161 time to fit residues: 19.3871 Evaluate side-chains 122 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 1133 HIS Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1215 LYS Chi-restraints excluded: chain A residue 1282 ILE Chi-restraints excluded: chain A residue 1570 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 9 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.125007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.100090 restraints weight = 16237.220| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.78 r_work: 0.3103 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10612 Z= 0.120 Angle : 0.506 8.676 14386 Z= 0.262 Chirality : 0.040 0.168 1611 Planarity : 0.004 0.060 1772 Dihedral : 5.737 129.647 1488 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 0.90 % Allowed : 9.44 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.24), residues: 1229 helix: 1.33 (0.20), residues: 663 sheet: -0.86 (0.51), residues: 99 loop : -1.44 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1301 TYR 0.021 0.001 TYR A 927 PHE 0.020 0.002 PHE A1186 TRP 0.014 0.001 TRP A 474 HIS 0.003 0.001 HIS A 743 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10612) covalent geometry : angle 0.50579 / 0.26 (14386) hydrogen bonds : bond 0.04228 / 2.72 ( 498) hydrogen bonds : angle 4.14427 / 2.98 ( 1443) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 561 MET cc_start: 0.8339 (mmt) cc_final: 0.8072 (mmm) REVERT: A 893 ARG cc_start: 0.6553 (ttt-90) cc_final: 0.6295 (ttt-90) REVERT: A 1120 TYR cc_start: 0.7875 (t80) cc_final: 0.7467 (t80) REVERT: A 1173 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5619 (pp) REVERT: A 1399 MET cc_start: 0.6184 (OUTLIER) cc_final: 0.5511 (ttt) outliers start: 10 outliers final: 5 residues processed: 124 average time/residue: 0.1088 time to fit residues: 18.5706 Evaluate side-chains 122 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 1133 HIS Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1399 MET Chi-restraints excluded: chain A residue 1570 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 0.0040 chunk 37 optimal weight: 0.6980 chunk 63 optimal weight: 0.1980 chunk 120 optimal weight: 4.9990 chunk 104 optimal weight: 0.0770 chunk 125 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.3750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 828 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 = 0.3584 r_free = 0.3584 target = 0.126859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.102139 restraints weight = 16163.983| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.76 r_work: 0.3136 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10612 Z= 0.100 Angle : 0.500 11.587 14386 Z= 0.255 Chirality : 0.039 0.169 1611 Planarity : 0.004 0.060 1772 Dihedral : 5.607 130.106 1488 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.69 % Favored : 97.23 % Rotamer: Outliers : 0.54 % Allowed : 9.98 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.24), residues: 1229 helix: 1.55 (0.20), residues: 660 sheet: -0.77 (0.51), residues: 99 loop : -1.39 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1301 TYR 0.016 0.001 TYR A 927 PHE 0.019 0.001 PHE A1186 TRP 0.014 0.001 TRP A 946 HIS 0.003 0.001 HIS A 743 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (10612) covalent geometry : angle 0.50025 / 0.26 (14386) hydrogen bonds : bond 0.03707 / 2.39 ( 498) hydrogen bonds : angle 4.03977 / 2.91 ( 1443) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 561 MET cc_start: 0.8232 (mmt) cc_final: 0.7996 (mmm) REVERT: A 893 ARG cc_start: 0.6429 (ttt-90) cc_final: 0.6226 (ttt-90) REVERT: A 1094 PHE cc_start: 0.7863 (p90) cc_final: 0.7627 (p90) REVERT: A 1173 LEU cc_start: 0.5989 (OUTLIER) cc_final: 0.5613 (pp) REVERT: A 1399 MET cc_start: 0.6095 (OUTLIER) cc_final: 0.5437 (ttt) REVERT: A 1508 ILE cc_start: 0.8214 (mt) cc_final: 0.7950 (mm) REVERT: A 1555 GLU cc_start: 0.7714 (mp0) cc_final: 0.6530 (tm-30) outliers start: 6 outliers final: 3 residues processed: 127 average time/residue: 0.0991 time to fit residues: 17.3398 Evaluate side-chains 123 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1399 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 120 optimal weight: 0.0050 chunk 21 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 0.0870 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 64 optimal weight: 0.0070 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1404 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.127373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.103371 restraints weight = 16122.907| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.75 r_work: 0.3149 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10612 Z= 0.102 Angle : 0.519 10.670 14386 Z= 0.262 Chirality : 0.039 0.168 1611 Planarity : 0.004 0.059 1772 Dihedral : 5.550 129.999 1488 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.08 % Rotamer: Outliers : 0.45 % Allowed : 10.34 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.24), residues: 1229 helix: 1.66 (0.20), residues: 660 sheet: -0.72 (0.51), residues: 99 loop : -1.31 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1301 TYR 0.013 0.001 TYR A 760 PHE 0.019 0.001 PHE A1437 TRP 0.014 0.001 TRP A 946 HIS 0.003 0.001 HIS A 743 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (10612) covalent geometry : angle 0.51850 / 0.26 (14386) hydrogen bonds : bond 0.03707 / 2.40 ( 498) hydrogen bonds : angle 4.00722 / 2.89 ( 1443) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 561 MET cc_start: 0.8174 (mmt) cc_final: 0.7942 (mmm) REVERT: A 861 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7585 (tp-100) REVERT: A 893 ARG cc_start: 0.6601 (ttt-90) cc_final: 0.6380 (ttt-90) REVERT: A 1094 PHE cc_start: 0.7901 (p90) cc_final: 0.7663 (p90) REVERT: A 1120 TYR cc_start: 0.7889 (t80) cc_final: 0.7526 (t80) REVERT: A 1173 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5656 (pp) REVERT: A 1378 ASP cc_start: 0.8068 (m-30) cc_final: 0.7859 (m-30) REVERT: A 1399 MET cc_start: 0.6086 (OUTLIER) cc_final: 0.5406 (ttt) outliers start: 5 outliers final: 3 residues processed: 121 average time/residue: 0.1111 time to fit residues: 18.3886 Evaluate side-chains 121 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1399 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 51 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 0.0270 chunk 109 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.0000 chunk 14 optimal weight: 0.9990 overall best weight: 0.4844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 828 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 = 0.3588 r_free = 0.3588 target = 0.126998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.102982 restraints weight = 16066.035| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.75 r_work: 0.3141 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10612 Z= 0.107 Angle : 0.518 10.307 14386 Z= 0.263 Chirality : 0.039 0.165 1611 Planarity : 0.004 0.059 1772 Dihedral : 5.535 129.317 1488 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 0.45 % Allowed : 10.61 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.24), residues: 1229 helix: 1.64 (0.20), residues: 669 sheet: -0.72 (0.51), residues: 99 loop : -1.28 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 918 TYR 0.028 0.001 TYR A1510 PHE 0.019 0.001 PHE A1186 TRP 0.013 0.001 TRP A 474 HIS 0.003 0.001 HIS A 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (10612) covalent geometry : angle 0.51780 / 0.26 (14386) hydrogen bonds : bond 0.03809 / 2.46 ( 498) hydrogen bonds : angle 4.01271 / 2.90 ( 1443) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7951 (tpt-90) cc_final: 0.7699 (tpt-90) REVERT: A 561 MET cc_start: 0.8227 (mmt) cc_final: 0.7989 (mmm) REVERT: A 927 TYR cc_start: 0.5844 (t80) cc_final: 0.5576 (t80) REVERT: A 1094 PHE cc_start: 0.7915 (p90) cc_final: 0.7679 (p90) REVERT: A 1120 TYR cc_start: 0.7912 (t80) cc_final: 0.7570 (t80) REVERT: A 1173 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5666 (pp) REVERT: A 1399 MET cc_start: 0.6071 (OUTLIER) cc_final: 0.5424 (ttt) REVERT: A 1572 VAL cc_start: 0.8194 (t) cc_final: 0.7844 (m) outliers start: 5 outliers final: 2 residues processed: 123 average time/residue: 0.1205 time to fit residues: 20.3828 Evaluate side-chains 117 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1399 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 92 optimal weight: 0.9980 chunk 105 optimal weight: 0.1980 chunk 123 optimal weight: 3.9990 chunk 117 optimal weight: 0.0370 chunk 115 optimal weight: 0.9990 chunk 90 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.4980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 828 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 = 0.3574 r_free = 0.3574 target = 0.126618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.101679 restraints weight = 16208.750| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.86 r_work: 0.3103 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10612 Z= 0.096 Angle : 0.499 10.263 14386 Z= 0.253 Chirality : 0.038 0.161 1611 Planarity : 0.004 0.059 1772 Dihedral : 5.471 129.398 1488 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.45 % Allowed : 10.88 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.24), residues: 1229 helix: 1.81 (0.20), residues: 662 sheet: -0.69 (0.50), residues: 99 loop : -1.21 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 918 TYR 0.024 0.001 TYR A1510 PHE 0.018 0.001 PHE A1186 TRP 0.014 0.001 TRP A 946 HIS 0.003 0.000 HIS A 743 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (10612) covalent geometry : angle 0.49939 / 0.25 (14386) hydrogen bonds : bond 0.03520 / 2.29 ( 498) hydrogen bonds : angle 3.95465 / 2.86 ( 1443) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2521.29 seconds wall clock time: 43 minutes 53.63 seconds (2633.63 seconds total)