Starting phenix.real_space_refine on Wed Jul 30 12:30:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vf5_31947/07_2025/7vf5_31947.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vf5_31947/07_2025/7vf5_31947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vf5_31947/07_2025/7vf5_31947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vf5_31947/07_2025/7vf5_31947.map" model { file = "/net/cci-nas-00/data/ceres_data/7vf5_31947/07_2025/7vf5_31947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vf5_31947/07_2025/7vf5_31947.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.085 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: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 7760 2.51 5 N 2076 2.21 5 O 2404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12313 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 9325 Classifications: {'peptide': 1188} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 1141} Chain breaks: 3 Chain: "C" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1494 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain: "D" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1494 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Time building chain proxies: 8.92, per 1000 atoms: 0.72 Number of scatterers: 12313 At special positions: 0 Unit cell: (104.96, 111.52, 144.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 2404 8.00 N 2076 7.00 C 7760 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: 3.01 Conformation dependent library (CDL) restraints added in 1.7 seconds 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2996 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 3 sheets defined 76.8% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 373 through 392 removed outlier: 4.251A pdb=" N GLY A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 384 " --> pdb=" O GLU A 380 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A 390 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 405 Processing helix chain 'A' and resid 406 through 421 removed outlier: 4.530A pdb=" N ILE A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LYS A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 440 Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.687A pdb=" N ALA A 444 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.553A pdb=" N GLU A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 removed outlier: 4.215A pdb=" N GLY A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 491 removed outlier: 4.016A pdb=" N GLU A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 513 removed outlier: 3.598A pdb=" N LYS A 500 " --> pdb=" O SER A 496 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 522 Processing helix chain 'A' and resid 529 through 539 Processing helix chain 'A' and resid 543 through 577 removed outlier: 3.635A pdb=" N THR A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 640 removed outlier: 3.925A pdb=" N LEU A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 668 through 679 removed outlier: 3.815A pdb=" N ARG A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 689 Processing helix chain 'A' and resid 691 through 697 removed outlier: 4.012A pdb=" N HIS A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 removed outlier: 4.032A pdb=" N LEU A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 702 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A 714 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 724 Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.738A pdb=" N LEU A 730 " --> pdb=" O GLU A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 750 Processing helix chain 'A' and resid 756 through 780 removed outlier: 3.592A pdb=" N PHE A 778 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 780 " --> pdb=" O SER A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 801 Processing helix chain 'A' and resid 802 through 804 No H-bonds generated for 'chain 'A' and resid 802 through 804' Processing helix chain 'A' and resid 805 through 816 Processing helix chain 'A' and resid 822 through 832 removed outlier: 3.609A pdb=" N LEU A 828 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 832 " --> pdb=" O LEU A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 862 Processing helix chain 'A' and resid 865 through 882 removed outlier: 3.743A pdb=" N GLU A 869 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN A 870 " --> pdb=" O GLN A 866 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ALA A 873 " --> pdb=" O GLU A 869 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER A 874 " --> pdb=" O GLN A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 895 removed outlier: 3.761A pdb=" N GLU A 890 " --> pdb=" O ALA A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 906 No H-bonds generated for 'chain 'A' and resid 904 through 906' Processing helix chain 'A' and resid 907 through 918 Processing helix chain 'A' and resid 928 through 941 removed outlier: 4.234A pdb=" N THR A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 966 removed outlier: 3.587A pdb=" N LEU A 958 " --> pdb=" O LEU A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 983 removed outlier: 3.867A pdb=" N VAL A 975 " --> pdb=" O THR A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 989 removed outlier: 3.682A pdb=" N ARG A 988 " --> pdb=" O THR A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1019 removed outlier: 3.844A pdb=" N GLU A1019 " --> pdb=" O THR A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1046 removed outlier: 4.198A pdb=" N THR A1039 " --> pdb=" O SER A1035 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET A1042 " --> pdb=" O VAL A1038 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A1046 " --> pdb=" O MET A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1070 removed outlier: 3.954A pdb=" N LYS A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A1060 " --> pdb=" O ASP A1056 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A1061 " --> pdb=" O GLU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1087 Processing helix chain 'A' and resid 1091 through 1100 Processing helix chain 'A' and resid 1105 through 1107 No H-bonds generated for 'chain 'A' and resid 1105 through 1107' Processing helix chain 'A' and resid 1108 through 1120 removed outlier: 3.695A pdb=" N GLU A1118 " --> pdb=" O ILE A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1153 removed outlier: 3.600A pdb=" N ILE A1137 " --> pdb=" O GLU A1133 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A1153 " --> pdb=" O MET A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1165 removed outlier: 3.699A pdb=" N GLU A1160 " --> pdb=" O LYS A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1184 removed outlier: 3.628A pdb=" N VAL A1182 " --> pdb=" O ARG A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1208 removed outlier: 3.850A pdb=" N ILE A1195 " --> pdb=" O THR A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1234 Processing helix chain 'A' and resid 1235 through 1247 Processing helix chain 'A' and resid 1253 through 1269 Processing helix chain 'A' and resid 1275 through 1292 removed outlier: 4.024A pdb=" N GLU A1281 " --> pdb=" O GLN A1277 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR A1282 " --> pdb=" O GLN A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1313 Processing helix chain 'A' and resid 1314 through 1316 No H-bonds generated for 'chain 'A' and resid 1314 through 1316' Processing helix chain 'A' and resid 1319 through 1336 Processing helix chain 'A' and resid 1340 through 1355 removed outlier: 3.631A pdb=" N LEU A1344 " --> pdb=" O SER A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1371 removed outlier: 3.837A pdb=" N ARG A1369 " --> pdb=" O LYS A1365 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS A1370 " --> pdb=" O SER A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1385 removed outlier: 3.502A pdb=" N THR A1385 " --> pdb=" O ARG A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1404 removed outlier: 3.652A pdb=" N ALA A1394 " --> pdb=" O THR A1390 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1442 Processing helix chain 'A' and resid 1447 through 1462 removed outlier: 3.606A pdb=" N LEU A1459 " --> pdb=" O GLU A1455 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL A1460 " --> pdb=" O LEU A1456 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A1461 " --> pdb=" O GLU A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1486 removed outlier: 4.009A pdb=" N ASP A1471 " --> pdb=" O ASP A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1514 Processing helix chain 'A' and resid 1554 through 1559 removed outlier: 4.304A pdb=" N LYS A1558 " --> pdb=" O GLU A1554 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N CYS A1559 " --> pdb=" O LEU A1555 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1554 through 1559' Processing helix chain 'A' and resid 1565 through 1572 removed outlier: 4.131A pdb=" N LEU A1569 " --> pdb=" O LEU A1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 98 Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 114 through 146 Processing helix chain 'C' and resid 151 through 176 Processing helix chain 'C' and resid 176 through 244 Processing helix chain 'C' and resid 245 through 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'D' and resid 65 through 98 removed outlier: 4.200A pdb=" N SER D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 145 Processing helix chain 'D' and resid 148 through 176 removed outlier: 3.561A pdb=" N SER D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 247 removed outlier: 3.835A pdb=" N GLU D 184 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLN D 245 " --> pdb=" O GLN D 241 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER D 247 " --> pdb=" O GLN D 243 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 657 through 658 Processing sheet with id=AA2, first strand: chain 'A' and resid 1126 through 1128 removed outlier: 5.904A pdb=" N MET A1126 " --> pdb=" O VAL A1519 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1549 through 1551 838 hydrogen bonds defined for protein. 2505 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.03 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4058 1.34 - 1.46: 1213 1.46 - 1.57: 7101 1.57 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 12489 Sorted by residual: bond pdb=" CA LEU A1552 " pdb=" CB LEU A1552 " ideal model delta sigma weight residual 1.525 1.550 -0.026 1.47e-02 4.63e+03 3.04e+00 bond pdb=" C VAL A1033 " pdb=" N PRO A1034 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.20e-02 6.94e+03 2.28e+00 bond pdb=" CG GLU A 380 " pdb=" CD GLU A 380 " ideal model delta sigma weight residual 1.516 1.481 0.035 2.50e-02 1.60e+03 1.91e+00 bond pdb=" CD GLU A 380 " pdb=" OE1 GLU A 380 " ideal model delta sigma weight residual 1.249 1.223 0.026 1.90e-02 2.77e+03 1.80e+00 bond pdb=" CG1 ILE A 855 " pdb=" CD1 ILE A 855 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.80e+00 ... (remaining 12484 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 16621 2.13 - 4.26: 211 4.26 - 6.39: 39 6.39 - 8.52: 4 8.52 - 10.66: 1 Bond angle restraints: 16876 Sorted by residual: angle pdb=" N ILE A 624 " pdb=" CA ILE A 624 " pdb=" C ILE A 624 " ideal model delta sigma weight residual 111.90 108.57 3.33 8.10e-01 1.52e+00 1.69e+01 angle pdb=" N GLU A 380 " pdb=" CA GLU A 380 " pdb=" CB GLU A 380 " ideal model delta sigma weight residual 110.39 116.98 -6.59 1.66e+00 3.63e-01 1.58e+01 angle pdb=" C ILE A 379 " pdb=" N GLU A 380 " pdb=" CA GLU A 380 " ideal model delta sigma weight residual 120.72 114.10 6.62 1.67e+00 3.59e-01 1.57e+01 angle pdb=" C PHE A1400 " pdb=" N MET A1401 " pdb=" CA MET A1401 " ideal model delta sigma weight residual 120.38 124.83 -4.45 1.37e+00 5.33e-01 1.05e+01 angle pdb=" N ILE D 180 " pdb=" CA ILE D 180 " pdb=" C ILE D 180 " ideal model delta sigma weight residual 112.80 109.13 3.67 1.15e+00 7.56e-01 1.02e+01 ... (remaining 16871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7047 17.95 - 35.89: 560 35.89 - 53.84: 116 53.84 - 71.78: 35 71.78 - 89.73: 11 Dihedral angle restraints: 7769 sinusoidal: 3193 harmonic: 4576 Sorted by residual: dihedral pdb=" CA GLN A1443 " pdb=" C GLN A1443 " pdb=" N SER A1444 " pdb=" CA SER A1444 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA HIS A1463 " pdb=" C HIS A1463 " pdb=" N SER A1464 " pdb=" CA SER A1464 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA SER A 965 " pdb=" C SER A 965 " pdb=" N ALA A 966 " pdb=" CA ALA A 966 " ideal model delta harmonic sigma weight residual 180.00 163.03 16.97 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 7766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1474 0.043 - 0.086: 439 0.086 - 0.128: 69 0.128 - 0.171: 6 0.171 - 0.214: 3 Chirality restraints: 1991 Sorted by residual: chirality pdb=" CB ILE A1250 " pdb=" CA ILE A1250 " pdb=" CG1 ILE A1250 " pdb=" CG2 ILE A1250 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CG LEU A 689 " pdb=" CB LEU A 689 " pdb=" CD1 LEU A 689 " pdb=" CD2 LEU A 689 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CB VAL A 865 " pdb=" CA VAL A 865 " pdb=" CG1 VAL A 865 " pdb=" CG2 VAL A 865 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.87e-01 ... (remaining 1988 not shown) Planarity restraints: 2168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 447 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO A 448 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 448 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 448 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1504 " -0.039 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO A1505 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A1505 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1505 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 145 " -0.012 2.00e-02 2.50e+03 1.34e-02 4.46e+00 pdb=" CG TRP C 145 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP C 145 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP C 145 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 145 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 145 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 145 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 145 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 145 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 145 " 0.001 2.00e-02 2.50e+03 ... (remaining 2165 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 548 2.73 - 3.27: 13115 3.27 - 3.81: 20562 3.81 - 4.36: 24564 4.36 - 4.90: 42391 Nonbonded interactions: 101180 Sorted by model distance: nonbonded pdb=" O ILE A 449 " pdb=" OG SER C 220 " model vdw 2.182 3.040 nonbonded pdb=" OE2 GLU A 518 " pdb=" OH TYR A 560 " model vdw 2.213 3.040 nonbonded pdb=" O GLY D 126 " pdb=" NE2 GLN D 130 " model vdw 2.219 3.120 nonbonded pdb=" OG SER A1507 " pdb=" OD1 ASN A1510 " model vdw 2.220 3.040 nonbonded pdb=" O LEU A1459 " pdb=" OG SER A1464 " model vdw 2.233 3.040 ... (remaining 101175 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.00 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: 3.060 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: 0.030 Extract box with map and model: 0.710 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.140 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 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 0.055 12489 Z= 0.152 Angle : 0.637 10.656 16876 Z= 0.351 Chirality : 0.040 0.214 1991 Planarity : 0.004 0.059 2168 Dihedral : 14.392 89.727 4773 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1544 helix: 1.01 (0.16), residues: 1128 sheet: None (None), residues: 0 loop : -1.31 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 145 HIS 0.011 0.001 HIS A 797 PHE 0.025 0.002 PHE A 738 TYR 0.013 0.001 TYR A 417 ARG 0.004 0.000 ARG A1268 Details of bonding type rmsd hydrogen bonds : bond 0.12456 ( 838) hydrogen bonds : angle 5.01615 ( 2505) covalent geometry : bond 0.00336 (12489) covalent geometry : angle 0.63664 (16876) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: C 109 ARG cc_start: 0.8619 (mtp-110) cc_final: 0.7845 (mtp180) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 1.1614 time to fit residues: 203.0166 Evaluate side-chains 101 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 2.9990 chunk 116 optimal weight: 0.0030 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 0.0070 chunk 89 optimal weight: 0.0070 chunk 139 optimal weight: 9.9990 overall best weight: 0.2626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 440 ASN A 542 GLN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1463 HIS A1510 ASN D 130 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.198293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.137398 restraints weight = 13425.266| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.89 r_work: 0.3831 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12489 Z= 0.125 Angle : 0.584 9.987 16876 Z= 0.288 Chirality : 0.037 0.166 1991 Planarity : 0.004 0.056 2168 Dihedral : 4.203 18.749 1639 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.27 % Allowed : 7.32 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.22), residues: 1544 helix: 1.26 (0.16), residues: 1161 sheet: None (None), residues: 0 loop : -1.45 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1532 HIS 0.005 0.001 HIS A1235 PHE 0.016 0.001 PHE A1362 TYR 0.011 0.001 TYR A 850 ARG 0.007 0.000 ARG A1268 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 838) hydrogen bonds : angle 3.86187 ( 2505) covalent geometry : bond 0.00269 (12489) covalent geometry : angle 0.58354 (16876) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 ASP cc_start: 0.8774 (t70) cc_final: 0.8373 (m-30) REVERT: A 488 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7371 (mm-30) REVERT: A 1083 GLU cc_start: 0.7302 (mp0) cc_final: 0.7035 (tp30) REVERT: A 1191 THR cc_start: 0.8706 (t) cc_final: 0.8195 (m) REVERT: A 1431 MET cc_start: 0.5500 (OUTLIER) cc_final: 0.5290 (tpt) REVERT: C 109 ARG cc_start: 0.8154 (mtp-110) cc_final: 0.7520 (mtp180) REVERT: C 225 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6449 (mm) outliers start: 32 outliers final: 6 residues processed: 142 average time/residue: 1.1258 time to fit residues: 177.0978 Evaluate side-chains 117 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1294 ASP Chi-restraints excluded: chain A residue 1431 MET Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 163 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 66 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN A 419 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.195915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.134401 restraints weight = 13514.012| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.92 r_work: 0.3785 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12489 Z= 0.140 Angle : 0.567 9.067 16876 Z= 0.280 Chirality : 0.038 0.143 1991 Planarity : 0.003 0.054 2168 Dihedral : 4.130 18.187 1639 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.77 % Allowed : 9.94 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.22), residues: 1544 helix: 1.34 (0.15), residues: 1160 sheet: None (None), residues: 0 loop : -1.42 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1532 HIS 0.007 0.001 HIS A 494 PHE 0.021 0.001 PHE A1362 TYR 0.012 0.001 TYR A 850 ARG 0.002 0.000 ARG A1515 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 838) hydrogen bonds : angle 3.70977 ( 2505) covalent geometry : bond 0.00335 (12489) covalent geometry : angle 0.56661 (16876) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 1.457 Fit side-chains revert: symmetry clash REVERT: A 390 ASP cc_start: 0.8761 (t70) cc_final: 0.8322 (m-30) REVERT: A 488 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7434 (mm-30) REVERT: A 513 MET cc_start: 0.7490 (mmm) cc_final: 0.7207 (mmm) REVERT: A 1191 THR cc_start: 0.8763 (t) cc_final: 0.8230 (m) REVERT: C 109 ARG cc_start: 0.8186 (mtp-110) cc_final: 0.7514 (mtp180) outliers start: 39 outliers final: 11 residues processed: 147 average time/residue: 1.0974 time to fit residues: 179.2388 Evaluate side-chains 119 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1511 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 163 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 102 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 53 optimal weight: 0.0170 chunk 141 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 814 HIS ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.196288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.134362 restraints weight = 13424.811| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.89 r_work: 0.3785 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12489 Z= 0.135 Angle : 0.568 10.486 16876 Z= 0.274 Chirality : 0.037 0.142 1991 Planarity : 0.003 0.056 2168 Dihedral : 4.060 18.808 1639 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.63 % Allowed : 12.22 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.22), residues: 1544 helix: 1.42 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -1.44 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 145 HIS 0.007 0.001 HIS A 494 PHE 0.014 0.001 PHE A1362 TYR 0.010 0.001 TYR A 850 ARG 0.002 0.000 ARG A1515 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 838) hydrogen bonds : angle 3.59000 ( 2505) covalent geometry : bond 0.00326 (12489) covalent geometry : angle 0.56756 (16876) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 ASP cc_start: 0.8751 (t70) cc_final: 0.8304 (m-30) REVERT: A 488 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7422 (mm-30) REVERT: A 513 MET cc_start: 0.7532 (mmm) cc_final: 0.7235 (mmm) REVERT: A 867 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.6190 (pmt) REVERT: A 880 LYS cc_start: 0.8034 (ttpp) cc_final: 0.7678 (mtpm) REVERT: A 903 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7653 (t80) REVERT: A 923 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.6936 (mtm) REVERT: A 1184 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7852 (tt) REVERT: A 1191 THR cc_start: 0.8749 (t) cc_final: 0.8174 (m) REVERT: C 109 ARG cc_start: 0.8183 (mtp-110) cc_final: 0.7520 (mtp180) REVERT: C 195 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.5714 (mp0) outliers start: 37 outliers final: 12 residues processed: 140 average time/residue: 1.1479 time to fit residues: 178.8028 Evaluate side-chains 124 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1294 ASP Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain A residue 1511 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 163 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 74 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 ASN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.195742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.131081 restraints weight = 13456.693| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.71 r_work: 0.3759 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12489 Z= 0.140 Angle : 0.559 10.718 16876 Z= 0.272 Chirality : 0.037 0.121 1991 Planarity : 0.003 0.055 2168 Dihedral : 4.024 18.149 1639 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.91 % Allowed : 12.71 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.22), residues: 1544 helix: 1.44 (0.15), residues: 1172 sheet: None (None), residues: 0 loop : -1.41 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 145 HIS 0.006 0.001 HIS A 494 PHE 0.016 0.001 PHE A1362 TYR 0.011 0.001 TYR A1518 ARG 0.002 0.000 ARG C 173 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 838) hydrogen bonds : angle 3.56246 ( 2505) covalent geometry : bond 0.00341 (12489) covalent geometry : angle 0.55898 (16876) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 1.357 Fit side-chains REVERT: A 390 ASP cc_start: 0.8735 (t70) cc_final: 0.8272 (m-30) REVERT: A 468 GLU cc_start: 0.7132 (pp20) cc_final: 0.6913 (pp20) REVERT: A 488 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7424 (mm-30) REVERT: A 513 MET cc_start: 0.7560 (mmm) cc_final: 0.7275 (mmm) REVERT: A 779 GLN cc_start: 0.7398 (mm-40) cc_final: 0.7156 (mt0) REVERT: A 867 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.6123 (pmt) REVERT: A 880 LYS cc_start: 0.7987 (ttpp) cc_final: 0.7631 (mtpm) REVERT: A 903 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7645 (t80) REVERT: A 906 ASN cc_start: 0.7507 (t0) cc_final: 0.7282 (m-40) REVERT: A 923 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7011 (mtm) REVERT: A 1184 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7881 (tt) REVERT: A 1191 THR cc_start: 0.8745 (t) cc_final: 0.8157 (m) REVERT: A 1217 GLN cc_start: 0.7131 (mt0) cc_final: 0.6925 (mm-40) REVERT: C 109 ARG cc_start: 0.8115 (mtp-110) cc_final: 0.7498 (mtp180) REVERT: C 195 GLU cc_start: 0.6357 (OUTLIER) cc_final: 0.5645 (mp0) outliers start: 41 outliers final: 12 residues processed: 144 average time/residue: 0.9932 time to fit residues: 159.3787 Evaluate side-chains 128 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1294 ASP Chi-restraints excluded: chain A residue 1511 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 163 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 118 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** 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 = 0.4507 r_free = 0.4507 target = 0.195449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.132397 restraints weight = 13695.432| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 3.18 r_work: 0.3759 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12489 Z= 0.147 Angle : 0.577 10.922 16876 Z= 0.278 Chirality : 0.037 0.120 1991 Planarity : 0.003 0.057 2168 Dihedral : 4.026 18.130 1639 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.77 % Allowed : 14.06 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.22), residues: 1544 helix: 1.44 (0.15), residues: 1168 sheet: None (None), residues: 0 loop : -1.45 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 145 HIS 0.007 0.001 HIS A 494 PHE 0.020 0.001 PHE A1362 TYR 0.013 0.001 TYR A1359 ARG 0.003 0.000 ARG C 173 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 838) hydrogen bonds : angle 3.57741 ( 2505) covalent geometry : bond 0.00359 (12489) covalent geometry : angle 0.57660 (16876) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 1.321 Fit side-chains REVERT: A 336 MET cc_start: 0.3513 (tmm) cc_final: 0.2943 (tpt) REVERT: A 390 ASP cc_start: 0.8691 (t70) cc_final: 0.8244 (m-30) REVERT: A 488 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7433 (mm-30) REVERT: A 513 MET cc_start: 0.7581 (mmm) cc_final: 0.7358 (mmm) REVERT: A 779 GLN cc_start: 0.7419 (mm-40) cc_final: 0.7187 (mt0) REVERT: A 867 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.6191 (pmt) REVERT: A 880 LYS cc_start: 0.8007 (ttpp) cc_final: 0.7658 (mtpm) REVERT: A 903 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7603 (t80) REVERT: A 923 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7026 (mtm) REVERT: A 1184 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7926 (tt) REVERT: A 1311 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6913 (tm-30) REVERT: A 1361 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6496 (tt) REVERT: C 109 ARG cc_start: 0.8118 (mtp-110) cc_final: 0.7504 (mtp180) REVERT: C 195 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5684 (mp0) outliers start: 39 outliers final: 18 residues processed: 143 average time/residue: 1.0825 time to fit residues: 172.9092 Evaluate side-chains 133 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1206 ASP Chi-restraints excluded: chain A residue 1294 ASP Chi-restraints excluded: chain A residue 1361 LEU Chi-restraints excluded: chain A residue 1511 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 163 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 114 optimal weight: 0.0370 chunk 54 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1175 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.196736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.132124 restraints weight = 13523.403| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 2.71 r_work: 0.3764 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12489 Z= 0.124 Angle : 0.564 12.211 16876 Z= 0.272 Chirality : 0.037 0.120 1991 Planarity : 0.003 0.059 2168 Dihedral : 3.972 18.666 1639 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.41 % Allowed : 15.41 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.22), residues: 1544 helix: 1.55 (0.15), residues: 1169 sheet: None (None), residues: 0 loop : -1.42 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 145 HIS 0.006 0.001 HIS A 494 PHE 0.017 0.001 PHE A1362 TYR 0.022 0.001 TYR A 341 ARG 0.003 0.000 ARG C 173 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 838) hydrogen bonds : angle 3.50664 ( 2505) covalent geometry : bond 0.00295 (12489) covalent geometry : angle 0.56426 (16876) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: A 336 MET cc_start: 0.3422 (tmm) cc_final: 0.3107 (tpt) REVERT: A 390 ASP cc_start: 0.8694 (t70) cc_final: 0.8229 (m-30) REVERT: A 488 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7395 (mm-30) REVERT: A 513 MET cc_start: 0.7557 (mmm) cc_final: 0.7311 (mmm) REVERT: A 656 MET cc_start: 0.8084 (tpp) cc_final: 0.7767 (tpt) REVERT: A 880 LYS cc_start: 0.7968 (ttpp) cc_final: 0.7659 (mtpm) REVERT: A 903 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7603 (t80) REVERT: A 997 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6528 (tp) REVERT: A 1083 GLU cc_start: 0.7311 (mp0) cc_final: 0.6896 (tp30) REVERT: A 1184 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7844 (tt) REVERT: A 1191 THR cc_start: 0.8639 (t) cc_final: 0.8159 (m) REVERT: A 1207 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6583 (mp) REVERT: A 1311 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6888 (tm-30) REVERT: A 1361 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6375 (tt) REVERT: C 109 ARG cc_start: 0.8013 (mtp-110) cc_final: 0.7441 (mtp180) REVERT: C 195 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.5632 (mp0) REVERT: D 84 GLU cc_start: 0.8147 (tp30) cc_final: 0.7411 (tt0) outliers start: 34 outliers final: 14 residues processed: 139 average time/residue: 1.0534 time to fit residues: 162.0616 Evaluate side-chains 128 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1294 ASP Chi-restraints excluded: chain A residue 1361 LEU Chi-restraints excluded: chain A residue 1511 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain D residue 90 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 136 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 139 optimal weight: 0.0670 chunk 65 optimal weight: 0.0030 overall best weight: 0.5928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** 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 = 0.4521 r_free = 0.4521 target = 0.196801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.132037 restraints weight = 13540.477| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.70 r_work: 0.3762 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12489 Z= 0.126 Angle : 0.578 12.840 16876 Z= 0.277 Chirality : 0.037 0.119 1991 Planarity : 0.003 0.058 2168 Dihedral : 3.982 18.108 1639 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.63 % Allowed : 15.84 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.22), residues: 1544 helix: 1.56 (0.15), residues: 1168 sheet: None (None), residues: 0 loop : -1.42 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1532 HIS 0.006 0.001 HIS A 494 PHE 0.035 0.001 PHE A1362 TYR 0.024 0.002 TYR A 341 ARG 0.003 0.000 ARG C 173 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 838) hydrogen bonds : angle 3.49501 ( 2505) covalent geometry : bond 0.00302 (12489) covalent geometry : angle 0.57846 (16876) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 1.458 Fit side-chains revert: symmetry clash REVERT: A 390 ASP cc_start: 0.8677 (t70) cc_final: 0.8173 (m-30) REVERT: A 488 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7400 (mm-30) REVERT: A 513 MET cc_start: 0.7564 (mmm) cc_final: 0.7291 (mmm) REVERT: A 656 MET cc_start: 0.8120 (tpp) cc_final: 0.7800 (tpt) REVERT: A 738 PHE cc_start: 0.6765 (m-80) cc_final: 0.5904 (m-80) REVERT: A 880 LYS cc_start: 0.7975 (ttpp) cc_final: 0.7680 (mtpm) REVERT: A 903 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7559 (t80) REVERT: A 997 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6552 (tp) REVERT: A 1184 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7846 (tt) REVERT: A 1191 THR cc_start: 0.8637 (t) cc_final: 0.8135 (m) REVERT: A 1207 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6581 (mp) REVERT: A 1311 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6894 (tm-30) REVERT: A 1361 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6530 (tt) REVERT: A 1457 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: C 109 ARG cc_start: 0.7989 (mtp-110) cc_final: 0.7444 (mtp180) REVERT: C 195 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.5625 (mp0) REVERT: D 84 GLU cc_start: 0.8113 (tp30) cc_final: 0.7388 (tt0) REVERT: D 87 MET cc_start: 0.6987 (mmm) cc_final: 0.6768 (mmm) outliers start: 37 outliers final: 13 residues processed: 138 average time/residue: 1.1511 time to fit residues: 175.3988 Evaluate side-chains 130 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1294 ASP Chi-restraints excluded: chain A residue 1361 LEU Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain A residue 1511 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain D residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 79 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** 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 = 0.4517 r_free = 0.4517 target = 0.196181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.131309 restraints weight = 13556.307| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.71 r_work: 0.3752 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12489 Z= 0.136 Angle : 0.597 13.364 16876 Z= 0.285 Chirality : 0.037 0.119 1991 Planarity : 0.004 0.059 2168 Dihedral : 3.984 18.171 1639 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.99 % Allowed : 16.76 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.22), residues: 1544 helix: 1.54 (0.15), residues: 1173 sheet: None (None), residues: 0 loop : -1.38 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1532 HIS 0.006 0.001 HIS A 494 PHE 0.016 0.001 PHE A1362 TYR 0.023 0.001 TYR A 341 ARG 0.004 0.000 ARG C 173 Details of bonding type rmsd hydrogen bonds : bond 0.03294 ( 838) hydrogen bonds : angle 3.48738 ( 2505) covalent geometry : bond 0.00331 (12489) covalent geometry : angle 0.59651 (16876) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: A 336 MET cc_start: 0.3515 (tmm) cc_final: 0.3029 (tpt) REVERT: A 390 ASP cc_start: 0.8659 (t70) cc_final: 0.8166 (m-30) REVERT: A 488 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7377 (mm-30) REVERT: A 513 MET cc_start: 0.7541 (mmm) cc_final: 0.7292 (mmm) REVERT: A 656 MET cc_start: 0.8120 (tpp) cc_final: 0.7863 (tpt) REVERT: A 738 PHE cc_start: 0.6723 (m-80) cc_final: 0.5866 (m-80) REVERT: A 779 GLN cc_start: 0.7342 (mm-40) cc_final: 0.7140 (mt0) REVERT: A 880 LYS cc_start: 0.7941 (ttpp) cc_final: 0.7650 (mtpm) REVERT: A 903 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7543 (t80) REVERT: A 997 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6545 (tp) REVERT: A 1083 GLU cc_start: 0.7275 (mp0) cc_final: 0.6929 (tp30) REVERT: A 1184 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7860 (tt) REVERT: A 1191 THR cc_start: 0.8644 (t) cc_final: 0.8144 (m) REVERT: A 1207 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6581 (mp) REVERT: A 1311 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6878 (tm-30) REVERT: A 1361 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6613 (tt) REVERT: C 87 MET cc_start: 0.5848 (tpp) cc_final: 0.5619 (mmp) REVERT: C 109 ARG cc_start: 0.8006 (mtp-110) cc_final: 0.7457 (mtp180) REVERT: C 145 TRP cc_start: 0.6546 (m100) cc_final: 0.5879 (m-90) REVERT: D 84 GLU cc_start: 0.8118 (tp30) cc_final: 0.7351 (tt0) outliers start: 28 outliers final: 15 residues processed: 134 average time/residue: 1.1116 time to fit residues: 164.2450 Evaluate side-chains 132 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1294 ASP Chi-restraints excluded: chain A residue 1358 ASP Chi-restraints excluded: chain A residue 1361 LEU Chi-restraints excluded: chain A residue 1511 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain D residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 110 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 29 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** 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 = 0.4519 r_free = 0.4519 target = 0.196491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.131609 restraints weight = 13476.897| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.71 r_work: 0.3784 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12489 Z= 0.132 Angle : 0.607 14.004 16876 Z= 0.289 Chirality : 0.037 0.129 1991 Planarity : 0.004 0.059 2168 Dihedral : 3.963 17.984 1639 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.49 % Allowed : 17.54 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.22), residues: 1544 helix: 1.61 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -1.37 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1532 HIS 0.006 0.001 HIS A 494 PHE 0.041 0.001 PHE A1362 TYR 0.024 0.001 TYR A 341 ARG 0.004 0.000 ARG C 173 Details of bonding type rmsd hydrogen bonds : bond 0.03310 ( 838) hydrogen bonds : angle 3.49801 ( 2505) covalent geometry : bond 0.00318 (12489) covalent geometry : angle 0.60745 (16876) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.449 Fit side-chains revert: symmetry clash REVERT: A 336 MET cc_start: 0.3611 (tmm) cc_final: 0.3151 (tpt) REVERT: A 390 ASP cc_start: 0.8654 (t70) cc_final: 0.8161 (m-30) REVERT: A 488 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7389 (mm-30) REVERT: A 513 MET cc_start: 0.7563 (mmm) cc_final: 0.7297 (mmm) REVERT: A 656 MET cc_start: 0.8039 (tpp) cc_final: 0.7785 (tpt) REVERT: A 738 PHE cc_start: 0.6756 (m-80) cc_final: 0.5873 (m-80) REVERT: A 880 LYS cc_start: 0.7974 (ttpp) cc_final: 0.7702 (mtpm) REVERT: A 903 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7518 (t80) REVERT: A 997 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6650 (tp) REVERT: A 1083 GLU cc_start: 0.7247 (mp0) cc_final: 0.7035 (tp30) REVERT: A 1184 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7843 (tt) REVERT: A 1191 THR cc_start: 0.8659 (t) cc_final: 0.8145 (m) REVERT: A 1311 GLU cc_start: 0.7425 (mm-30) cc_final: 0.6975 (tm-30) REVERT: A 1361 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6803 (tt) REVERT: A 1457 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7646 (pm20) REVERT: C 87 MET cc_start: 0.6025 (tpp) cc_final: 0.5803 (mmp) REVERT: C 109 ARG cc_start: 0.8046 (mtp-110) cc_final: 0.7495 (mtp180) REVERT: D 84 GLU cc_start: 0.8171 (tp30) cc_final: 0.7404 (tt0) outliers start: 21 outliers final: 14 residues processed: 129 average time/residue: 1.1624 time to fit residues: 167.5706 Evaluate side-chains 131 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1294 ASP Chi-restraints excluded: chain A residue 1361 LEU Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain A residue 1511 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain D residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 47 optimal weight: 0.0870 chunk 62 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.211882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.133164 restraints weight = 13987.217| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.97 r_work: 0.3677 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12489 Z= 0.217 Angle : 0.675 14.087 16876 Z= 0.323 Chirality : 0.041 0.147 1991 Planarity : 0.004 0.058 2168 Dihedral : 4.179 19.414 1639 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.99 % Allowed : 17.54 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.22), residues: 1544 helix: 1.32 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -1.34 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1532 HIS 0.008 0.001 HIS A1363 PHE 0.016 0.002 PHE A1362 TYR 0.030 0.002 TYR A 341 ARG 0.003 0.000 ARG C 173 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 838) hydrogen bonds : angle 3.67593 ( 2505) covalent geometry : bond 0.00547 (12489) covalent geometry : angle 0.67548 (16876) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7974.81 seconds wall clock time: 138 minutes 56.44 seconds (8336.44 seconds total)