Starting phenix.real_space_refine on Fri Oct 23 16:34:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vsv_65308/10_2026/9vsv_65308.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vsv_65308/10_2026/9vsv_65308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vsv_65308/10_2026/9vsv_65308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vsv_65308/10_2026/9vsv_65308.map" model { file = "/net/cci-nas-00/data/ceres_data/9vsv_65308/10_2026/9vsv_65308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vsv_65308/10_2026/9vsv_65308.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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 62 5.16 5 C 6584 2.51 5 N 1683 2.21 5 O 1846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10175 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1271, 10148 Classifications: {'peptide': 1271} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1216} Chain breaks: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'CC9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.43, per 1000 atoms: 0.24 Number of scatterers: 10175 At special positions: 0 Unit cell: (75.331, 102.917, 145.357, 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 62 16.00 O 1846 8.00 N 1683 7.00 C 6584 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 712 " - pdb=" SG CYS A 732 " distance=2.02 Simple disulfide: pdb=" SG CYS A1402 " - pdb=" SG CYS A1444 " distance=2.02 Simple disulfide: pdb=" SG CYS A1418 " - pdb=" SG CYS A1441 " distance=2.02 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: 0.82 Conformation dependent library (CDL) restraints added in 371.2 milliseconds 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 8 sheets defined 61.0% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 247 through 258 Processing helix chain 'A' and resid 269 through 285 Processing helix chain 'A' and resid 286 through 291 removed outlier: 4.454A pdb=" N HIS A 289 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 291 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.730A pdb=" N LYS A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.612A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 390 through 399 Processing helix chain 'A' and resid 407 through 415 Processing helix chain 'A' and resid 434 through 445 Processing helix chain 'A' and resid 445 through 463 Processing helix chain 'A' and resid 492 through 511 Processing helix chain 'A' and resid 512 through 533 removed outlier: 3.560A pdb=" N VAL A 532 " --> pdb=" O ILE A 528 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 542 through 559 Processing helix chain 'A' and resid 560 through 562 No H-bonds generated for 'chain 'A' and resid 560 through 562' Processing helix chain 'A' and resid 563 through 581 removed outlier: 4.038A pdb=" N SER A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Proline residue: A 573 - end of helix Processing helix chain 'A' and resid 585 through 616 Proline residue: A 599 - end of helix removed outlier: 4.023A pdb=" N VAL A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 650 removed outlier: 3.589A pdb=" N PHE A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 670 Proline residue: A 659 - end of helix removed outlier: 3.722A pdb=" N VAL A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 665 " --> pdb=" O THR A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 680 Processing helix chain 'A' and resid 684 through 691 removed outlier: 3.543A pdb=" N ASN A 688 " --> pdb=" O SER A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 706 removed outlier: 3.903A pdb=" N TYR A 695 " --> pdb=" O ASN A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 761 Processing helix chain 'A' and resid 762 through 785 removed outlier: 3.554A pdb=" N GLU A 784 " --> pdb=" O ILE A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 909 Processing helix chain 'A' and resid 932 through 936 Processing helix chain 'A' and resid 951 through 964 Processing helix chain 'A' and resid 969 through 984 Processing helix chain 'A' and resid 1002 through 1016 Processing helix chain 'A' and resid 1033 through 1050 Processing helix chain 'A' and resid 1062 through 1067 removed outlier: 3.517A pdb=" N ALA A1067 " --> pdb=" O ALA A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1090 No H-bonds generated for 'chain 'A' and resid 1088 through 1090' Processing helix chain 'A' and resid 1091 through 1101 Processing helix chain 'A' and resid 1111 through 1120 removed outlier: 3.997A pdb=" N LEU A1117 " --> pdb=" O ALA A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1138 Processing helix chain 'A' and resid 1139 through 1157 removed outlier: 3.706A pdb=" N GLN A1143 " --> pdb=" O SER A1139 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A1157 " --> pdb=" O GLU A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1168 Processing helix chain 'A' and resid 1174 through 1193 Processing helix chain 'A' and resid 1195 through 1215 Processing helix chain 'A' and resid 1221 through 1236 removed outlier: 3.594A pdb=" N GLN A1226 " --> pdb=" O MET A1222 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A1236 " --> pdb=" O VAL A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1260 Proline residue: A1248 - end of helix Processing helix chain 'A' and resid 1268 through 1300 removed outlier: 3.773A pdb=" N GLU A1280 " --> pdb=" O GLN A1276 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A1281 " --> pdb=" O ILE A1277 " (cutoff:3.500A) Proline residue: A1282 - end of helix removed outlier: 4.018A pdb=" N TYR A1297 " --> pdb=" O PHE A1293 " (cutoff:3.500A) Proline residue: A1298 - end of helix Processing helix chain 'A' and resid 1301 through 1306 removed outlier: 3.706A pdb=" N ALA A1305 " --> pdb=" O LEU A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1338 Processing helix chain 'A' and resid 1342 through 1360 Processing helix chain 'A' and resid 1371 through 1373 No H-bonds generated for 'chain 'A' and resid 1371 through 1373' Processing helix chain 'A' and resid 1374 through 1380 Processing helix chain 'A' and resid 1381 through 1396 removed outlier: 4.114A pdb=" N TYR A1385 " --> pdb=" O ASN A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1430 Proline residue: A1424 - end of helix removed outlier: 4.012A pdb=" N PHE A1428 " --> pdb=" O PRO A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1456 removed outlier: 4.260A pdb=" N PHE A1452 " --> pdb=" O SER A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1489 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 177 removed outlier: 6.031A pdb=" N ILE A 169 " --> pdb=" O TYR A 131 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR A 131 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS A 171 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG A 129 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N MET A 173 " --> pdb=" O ASN A 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 168 through 177 removed outlier: 6.031A pdb=" N ILE A 169 " --> pdb=" O TYR A 131 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR A 131 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS A 171 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG A 129 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N MET A 173 " --> pdb=" O ASN A 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 236 removed outlier: 6.868A pdb=" N ILE A 234 " --> pdb=" O CYS A 325 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ASP A 327 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N SER A 236 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 374 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE A 385 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 376 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AA5, first strand: chain 'A' and resid 715 through 716 Processing sheet with id=AA6, first strand: chain 'A' and resid 873 through 885 removed outlier: 6.440A pdb=" N TYR A 866 " --> pdb=" O ILE A 877 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP A 879 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A 864 " --> pdb=" O ASP A 879 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL A 881 " --> pdb=" O ARG A 862 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG A 862 " --> pdb=" O VAL A 881 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY A 883 " --> pdb=" O PHE A 860 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE A 860 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A 864 " --> pdb=" O ASP A 919 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASP A 919 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR A 866 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE A 917 " --> pdb=" O TYR A 866 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 937 through 940 removed outlier: 6.309A pdb=" N LEU A1023 " --> pdb=" O LEU A1055 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N THR A1057 " --> pdb=" O LEU A1023 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU A1025 " --> pdb=" O THR A1057 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE A 890 " --> pdb=" O ARG A1071 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU A1073 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA A 892 " --> pdb=" O LEU A1073 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU A1075 " --> pdb=" O ALA A 892 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N MET A 894 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLN A1076 " --> pdb=" O THR A1081 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N THR A1081 " --> pdb=" O GLN A1076 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1408 through 1410 571 hydrogen bonds defined for protein. 1644 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: 1.76 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2504 1.33 - 1.45: 2214 1.45 - 1.57: 5623 1.57 - 1.70: 0 1.70 - 1.82: 101 Bond restraints: 10442 Sorted by residual: bond pdb=" C2 CC9 A1601 " pdb=" C3 CC9 A1601 " ideal model delta sigma weight residual 1.343 1.555 -0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C13 CC9 A1601 " pdb=" C14 CC9 A1601 " ideal model delta sigma weight residual 1.344 1.552 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C3 CC9 A1601 " pdb=" C4 CC9 A1601 " ideal model delta sigma weight residual 1.452 1.532 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C14 CC9 A1601 " pdb=" C15 CC9 A1601 " ideal model delta sigma weight residual 1.452 1.527 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" CZ ARG A1045 " pdb=" NH2 ARG A1045 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.90e+00 ... (remaining 10437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 13177 3.10 - 6.20: 966 6.20 - 9.30: 15 9.30 - 12.40: 3 12.40 - 15.50: 1 Bond angle restraints: 14162 Sorted by residual: angle pdb=" CA PHE A 167 " pdb=" CB PHE A 167 " pdb=" CG PHE A 167 " ideal model delta sigma weight residual 113.80 120.74 -6.94 1.00e+00 1.00e+00 4.82e+01 angle pdb=" C GLY A 719 " pdb=" N PRO A 720 " pdb=" CA PRO A 720 " ideal model delta sigma weight residual 119.84 127.98 -8.14 1.25e+00 6.40e-01 4.24e+01 angle pdb=" CA ASP A 298 " pdb=" CB ASP A 298 " pdb=" CG ASP A 298 " ideal model delta sigma weight residual 112.60 118.16 -5.56 1.00e+00 1.00e+00 3.09e+01 angle pdb=" C VAL A 431 " pdb=" N PRO A 432 " pdb=" CA PRO A 432 " ideal model delta sigma weight residual 119.90 125.35 -5.45 1.02e+00 9.61e-01 2.85e+01 angle pdb=" C13 CC9 A1601 " pdb=" C14 CC9 A1601 " pdb=" C15 CC9 A1601 " ideal model delta sigma weight residual 126.98 111.48 15.50 3.00e+00 1.11e-01 2.67e+01 ... (remaining 14157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 5663 16.76 - 33.51: 358 33.51 - 50.27: 64 50.27 - 67.02: 31 67.02 - 83.77: 10 Dihedral angle restraints: 6126 sinusoidal: 2422 harmonic: 3704 Sorted by residual: dihedral pdb=" C ASN A1220 " pdb=" N ASN A1220 " pdb=" CA ASN A1220 " pdb=" CB ASN A1220 " ideal model delta harmonic sigma weight residual -122.60 -138.43 15.83 0 2.50e+00 1.60e-01 4.01e+01 dihedral pdb=" C ILE A 514 " pdb=" N ILE A 514 " pdb=" CA ILE A 514 " pdb=" CB ILE A 514 " ideal model delta harmonic sigma weight residual -122.00 -135.82 13.82 0 2.50e+00 1.60e-01 3.06e+01 dihedral pdb=" CA GLU A1086 " pdb=" C GLU A1086 " pdb=" N LEU A1087 " pdb=" CA LEU A1087 " ideal model delta harmonic sigma weight residual 180.00 153.61 26.39 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 6123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1208 0.112 - 0.223: 278 0.223 - 0.335: 39 0.335 - 0.447: 4 0.447 - 0.558: 2 Chirality restraints: 1531 Sorted by residual: chirality pdb=" CA ASN A1220 " pdb=" N ASN A1220 " pdb=" C ASN A1220 " pdb=" CB ASN A1220 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.79e+00 chirality pdb=" CA ASP A1438 " pdb=" N ASP A1438 " pdb=" C ASP A1438 " pdb=" CB ASP A1438 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" CA ILE A 514 " pdb=" N ILE A 514 " pdb=" C ILE A 514 " pdb=" CB ILE A 514 " both_signs ideal model delta sigma weight residual False 2.43 2.05 0.39 2.00e-01 2.50e+01 3.72e+00 ... (remaining 1528 not shown) Planarity restraints: 1806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 CC9 A1601 " -0.136 2.00e-02 2.50e+03 2.97e-01 8.82e+02 pdb=" C2 CC9 A1601 " 0.379 2.00e-02 2.50e+03 pdb=" C3 CC9 A1601 " -0.405 2.00e-02 2.50e+03 pdb=" C4 CC9 A1601 " 0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 CC9 A1601 " -0.280 2.00e-02 2.50e+03 2.70e-01 7.30e+02 pdb=" C13 CC9 A1601 " 0.314 2.00e-02 2.50e+03 pdb=" C14 CC9 A1601 " 0.222 2.00e-02 2.50e+03 pdb=" C15 CC9 A1601 " -0.256 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1485 " -0.132 2.00e-02 2.50e+03 7.74e-02 1.20e+02 pdb=" CG TYR A1485 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A1485 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 TYR A1485 " 0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR A1485 " 0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR A1485 " 0.056 2.00e-02 2.50e+03 pdb=" CZ TYR A1485 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR A1485 " -0.131 2.00e-02 2.50e+03 ... (remaining 1803 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 5176 3.01 - 3.48: 10579 3.48 - 3.95: 17381 3.95 - 4.43: 19787 4.43 - 4.90: 32363 Nonbonded interactions: 85286 Sorted by model distance: nonbonded pdb=" OD1 ASP A 930 " pdb=" OG SER A 932 " model vdw 2.534 3.040 nonbonded pdb=" OE2 GLU A 564 " pdb=" OG SER A 640 " model vdw 2.543 3.040 nonbonded pdb=" OH TYR A1407 " pdb=" OE2 GLU A1434 " model vdw 2.553 3.040 nonbonded pdb=" OD1 ASP A1438 " pdb=" OG SER A1440 " model vdw 2.562 3.040 nonbonded pdb=" OG SER A 194 " pdb=" OD2 ASP A 327 " model vdw 2.562 3.040 ... (remaining 85281 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.370 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 : 0.013 0.212 10445 Z= 0.736 Angle : 1.711 15.498 14168 Z= 1.170 Chirality : 0.095 0.558 1531 Planarity : 0.018 0.297 1806 Dihedral : 12.929 83.775 3747 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 0.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.46 % Favored : 97.30 % Rotamer: Outliers : 1.38 % Allowed : 2.86 % Favored : 95.76 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 1.85 % 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: -0.67 (0.21), residues: 1261 helix: -0.51 (0.17), residues: 684 sheet: -0.20 (0.50), residues: 75 loop : -0.10 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 763 TYR 0.132 0.019 TYR A1485 PHE 0.115 0.015 PHE A 552 TRP 0.109 0.023 TRP A1319 HIS 0.013 0.003 HIS A 880 Details of bonding type rmsd/Z covalent geometry : bond 0.01250 / 0.74 (10442) covalent geometry : angle 1.71105 / 1.17 (14162) SS BOND : bond 0.01128 / 0.56 ( 3) SS BOND : angle 2.24173 / 1.02 ( 6) hydrogen bonds : bond 0.16649 / 11.16 ( 566) hydrogen bonds : angle 7.18579 / 5.04 ( 1644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.8811 (mpt) cc_final: 0.8565 (mpt) REVERT: A 203 ASN cc_start: 0.8805 (OUTLIER) cc_final: 0.8487 (t0) REVERT: A 214 GLN cc_start: 0.7870 (mt0) cc_final: 0.7420 (mt0) REVERT: A 238 GLU cc_start: 0.7826 (tt0) cc_final: 0.7523 (tt0) REVERT: A 298 ASP cc_start: 0.8504 (p0) cc_final: 0.8192 (p0) REVERT: A 299 PHE cc_start: 0.8408 (m-80) cc_final: 0.8066 (m-80) REVERT: A 364 SER cc_start: 0.8712 (t) cc_final: 0.8485 (p) REVERT: A 410 ASP cc_start: 0.8423 (m-30) cc_final: 0.8199 (m-30) REVERT: A 439 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6952 (tm-30) REVERT: A 495 MET cc_start: 0.8326 (mmt) cc_final: 0.8038 (mmp) REVERT: A 566 MET cc_start: 0.8899 (mmm) cc_final: 0.8597 (mmm) REVERT: A 570 GLU cc_start: 0.8480 (tt0) cc_final: 0.8240 (tp30) REVERT: A 657 MET cc_start: 0.8357 (mmm) cc_final: 0.7819 (mpp) REVERT: A 683 TRP cc_start: 0.8936 (p-90) cc_final: 0.8509 (p-90) REVERT: A 704 GLU cc_start: 0.9133 (tp30) cc_final: 0.8601 (tp30) REVERT: A 731 VAL cc_start: 0.9421 (OUTLIER) cc_final: 0.9147 (p) REVERT: A 893 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9082 (tt) REVERT: A 999 GLU cc_start: 0.8050 (pt0) cc_final: 0.7675 (pm20) REVERT: A 1042 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8316 (mmtt) REVERT: A 1077 LYS cc_start: 0.8857 (tmtt) cc_final: 0.8650 (tptp) REVERT: A 1114 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8399 (mt-10) REVERT: A 1162 ASP cc_start: 0.8339 (p0) cc_final: 0.8107 (p0) REVERT: A 1229 MET cc_start: 0.9257 (ttp) cc_final: 0.9038 (ttp) REVERT: A 1337 MET cc_start: 0.9431 (tpt) cc_final: 0.9147 (tpp) outliers start: 15 outliers final: 3 residues processed: 172 average time/residue: 0.6390 time to fit residues: 117.2408 Evaluate side-chains 114 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 1042 LYS Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain A residue 1428 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [108, 49, 97, 113, 53, 5, 33, 123, 65, 62, 51] chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 404 GLN A 444 ASN A 880 HIS A1138 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.109442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.086801 restraints weight = 15337.790| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.55 r_work: 0.2904 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10445 Z= 0.161 Angle : 0.643 12.588 14168 Z= 0.331 Chirality : 0.045 0.179 1531 Planarity : 0.004 0.037 1806 Dihedral : 6.566 57.275 1424 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.90 % Favored : 98.02 % Rotamer: Outliers : 1.75 % Allowed : 8.12 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.07 (0.23), residues: 1261 helix: 1.30 (0.19), residues: 693 sheet: -0.55 (0.47), residues: 100 loop : 0.27 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 498 TYR 0.016 0.002 TYR A1101 PHE 0.019 0.002 PHE A 552 TRP 0.013 0.001 TRP A 683 HIS 0.004 0.001 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (10442) covalent geometry : angle 0.64247 / 0.33 (14162) SS BOND : bond 0.00377 / 0.19 ( 3) SS BOND : angle 1.23737 / 0.48 ( 6) hydrogen bonds : bond 0.04738 / 3.15 ( 566) hydrogen bonds : angle 4.67714 / 3.28 ( 1644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.417 Fit side-chains REVERT: A 177 MET cc_start: 0.8524 (mpt) cc_final: 0.8261 (mpt) REVERT: A 203 ASN cc_start: 0.8829 (OUTLIER) cc_final: 0.8508 (t0) REVERT: A 298 ASP cc_start: 0.8446 (p0) cc_final: 0.8130 (p0) REVERT: A 299 PHE cc_start: 0.8502 (m-80) cc_final: 0.8271 (m-10) REVERT: A 331 ARG cc_start: 0.8275 (ttp80) cc_final: 0.8015 (ttt90) REVERT: A 495 MET cc_start: 0.8440 (mmt) cc_final: 0.8227 (mmt) REVERT: A 550 MET cc_start: 0.9150 (tpt) cc_final: 0.8880 (tpt) REVERT: A 566 MET cc_start: 0.8724 (mmm) cc_final: 0.8475 (mmm) REVERT: A 570 GLU cc_start: 0.8612 (tt0) cc_final: 0.8315 (tp30) REVERT: A 657 MET cc_start: 0.8303 (mmm) cc_final: 0.7776 (mpp) REVERT: A 670 TYR cc_start: 0.9223 (m-80) cc_final: 0.8891 (m-80) REVERT: A 683 TRP cc_start: 0.8819 (p-90) cc_final: 0.8436 (p-90) REVERT: A 999 GLU cc_start: 0.7844 (pt0) cc_final: 0.7246 (pm20) REVERT: A 1042 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8314 (mmtt) REVERT: A 1077 LYS cc_start: 0.8941 (tmtt) cc_final: 0.8739 (tptp) REVERT: A 1109 GLU cc_start: 0.8606 (pm20) cc_final: 0.8399 (pm20) outliers start: 19 outliers final: 8 residues processed: 125 average time/residue: 0.5136 time to fit residues: 69.7037 Evaluate side-chains 106 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 1042 LYS Chi-restraints excluded: chain A residue 1062 SER Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1417 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [100, 109, 91, 114, 74, 53, 92, 99, 102, 14, 48] chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 0.1980 chunk 92 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1189 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.109420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.086963 restraints weight = 15435.371| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.56 r_work: 0.2912 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10445 Z= 0.140 Angle : 0.558 9.726 14168 Z= 0.286 Chirality : 0.043 0.174 1531 Planarity : 0.004 0.039 1806 Dihedral : 6.063 78.235 1415 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.14 % Favored : 97.78 % Rotamer: Outliers : 2.03 % Allowed : 9.69 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.31 (0.23), residues: 1261 helix: 1.61 (0.19), residues: 695 sheet: -0.73 (0.48), residues: 100 loop : 0.24 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 498 TYR 0.015 0.001 TYR A1101 PHE 0.017 0.002 PHE A 552 TRP 0.013 0.001 TRP A 634 HIS 0.002 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (10442) covalent geometry : angle 0.55750 / 0.29 (14162) SS BOND : bond 0.00215 / 0.11 ( 3) SS BOND : angle 0.95079 / 0.40 ( 6) hydrogen bonds : bond 0.04264 / 2.83 ( 566) hydrogen bonds : angle 4.40098 / 3.09 ( 1644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.269 Fit side-chains REVERT: A 298 ASP cc_start: 0.8351 (p0) cc_final: 0.8031 (p0) REVERT: A 299 PHE cc_start: 0.8457 (m-80) cc_final: 0.8210 (m-10) REVERT: A 564 GLU cc_start: 0.7731 (pt0) cc_final: 0.7443 (pt0) REVERT: A 567 SER cc_start: 0.8911 (m) cc_final: 0.8500 (p) REVERT: A 570 GLU cc_start: 0.8847 (tt0) cc_final: 0.8468 (tp30) REVERT: A 657 MET cc_start: 0.8239 (mmm) cc_final: 0.7733 (mpp) REVERT: A 670 TYR cc_start: 0.9205 (m-80) cc_final: 0.8944 (m-80) REVERT: A 683 TRP cc_start: 0.8794 (p-90) cc_final: 0.8408 (p-90) REVERT: A 742 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: A 894 MET cc_start: 0.9315 (OUTLIER) cc_final: 0.9075 (ttm) REVERT: A 1042 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8316 (mmtt) REVERT: A 1109 GLU cc_start: 0.8596 (pm20) cc_final: 0.8378 (pm20) outliers start: 22 outliers final: 7 residues processed: 114 average time/residue: 0.5320 time to fit residues: 65.6882 Evaluate side-chains 107 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain A residue 1042 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [39, 106, 20, 38, 92, 16, 91, 84, 112, 67, 19] chunk 39 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 67 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1189 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.109146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.086736 restraints weight = 15506.524| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.56 r_work: 0.2912 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10445 Z= 0.148 Angle : 0.534 8.557 14168 Z= 0.274 Chirality : 0.043 0.219 1531 Planarity : 0.004 0.043 1806 Dihedral : 5.979 87.377 1413 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.98 % Favored : 97.94 % Rotamer: Outliers : 2.21 % Allowed : 10.70 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.39 (0.24), residues: 1261 helix: 1.71 (0.19), residues: 696 sheet: -0.55 (0.48), residues: 105 loop : 0.19 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 301 TYR 0.015 0.001 TYR A1101 PHE 0.018 0.002 PHE A1428 TRP 0.012 0.001 TRP A 634 HIS 0.002 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (10442) covalent geometry : angle 0.53372 / 0.27 (14162) SS BOND : bond 0.00208 / 0.10 ( 3) SS BOND : angle 0.86320 / 0.36 ( 6) hydrogen bonds : bond 0.04013 / 2.65 ( 566) hydrogen bonds : angle 4.26226 / 2.99 ( 1644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 298 ASP cc_start: 0.8279 (p0) cc_final: 0.7895 (p0) REVERT: A 299 PHE cc_start: 0.8468 (m-80) cc_final: 0.8243 (m-10) REVERT: A 567 SER cc_start: 0.8849 (m) cc_final: 0.8480 (p) REVERT: A 570 GLU cc_start: 0.8877 (tt0) cc_final: 0.8534 (tm-30) REVERT: A 657 MET cc_start: 0.8343 (mmm) cc_final: 0.7841 (mpp) REVERT: A 670 TYR cc_start: 0.9231 (m-80) cc_final: 0.9027 (m-80) REVERT: A 683 TRP cc_start: 0.8827 (p-90) cc_final: 0.8532 (p-90) REVERT: A 742 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: A 894 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.9031 (ttm) REVERT: A 1014 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8329 (tp30) REVERT: A 1042 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8324 (mmtt) REVERT: A 1109 GLU cc_start: 0.8596 (pm20) cc_final: 0.8381 (pm20) REVERT: A 1299 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8588 (mp) outliers start: 24 outliers final: 9 residues processed: 120 average time/residue: 0.5278 time to fit residues: 68.8695 Evaluate side-chains 107 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1042 LYS Chi-restraints excluded: chain A residue 1062 SER Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1311 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [7, 5, 81, 55, 16, 12, 79, 70, 60, 107, 117] chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.0970 chunk 79 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 107 optimal weight: 0.2980 chunk 117 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1189 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.109687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.087228 restraints weight = 15412.389| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.56 r_work: 0.2920 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10445 Z= 0.131 Angle : 0.519 8.954 14168 Z= 0.264 Chirality : 0.042 0.232 1531 Planarity : 0.004 0.046 1806 Dihedral : 6.013 88.256 1413 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.98 % Favored : 97.94 % Rotamer: Outliers : 2.58 % Allowed : 11.07 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.50 (0.24), residues: 1261 helix: 1.86 (0.19), residues: 694 sheet: -0.49 (0.49), residues: 104 loop : 0.12 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 129 TYR 0.013 0.001 TYR A1101 PHE 0.020 0.001 PHE A1428 TRP 0.011 0.001 TRP A 634 HIS 0.002 0.000 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10442) covalent geometry : angle 0.51833 / 0.26 (14162) SS BOND : bond 0.00193 / 0.09 ( 3) SS BOND : angle 0.96597 / 0.41 ( 6) hydrogen bonds : bond 0.03812 / 2.52 ( 566) hydrogen bonds : angle 4.17625 / 2.92 ( 1644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.416 Fit side-chains REVERT: A 227 ARG cc_start: 0.8430 (ttp-170) cc_final: 0.8064 (ptp-110) REVERT: A 298 ASP cc_start: 0.8231 (p0) cc_final: 0.7838 (p0) REVERT: A 299 PHE cc_start: 0.8478 (m-80) cc_final: 0.8270 (m-10) REVERT: A 439 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7027 (tm-30) REVERT: A 564 GLU cc_start: 0.7559 (pt0) cc_final: 0.7275 (pt0) REVERT: A 567 SER cc_start: 0.8818 (m) cc_final: 0.8461 (p) REVERT: A 570 GLU cc_start: 0.8913 (tt0) cc_final: 0.8492 (tp30) REVERT: A 657 MET cc_start: 0.8340 (mmm) cc_final: 0.7815 (mpp) REVERT: A 670 TYR cc_start: 0.9244 (m-80) cc_final: 0.9041 (m-80) REVERT: A 683 TRP cc_start: 0.8869 (p-90) cc_final: 0.8550 (p-90) REVERT: A 742 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: A 894 MET cc_start: 0.9278 (OUTLIER) cc_final: 0.9033 (ttm) REVERT: A 1014 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8353 (tp30) REVERT: A 1042 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8348 (mmtt) REVERT: A 1109 GLU cc_start: 0.8617 (pm20) cc_final: 0.8416 (pm20) REVERT: A 1299 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8587 (mp) outliers start: 28 outliers final: 16 residues processed: 115 average time/residue: 0.5374 time to fit residues: 67.0055 Evaluate side-chains 116 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain A residue 921 GLU Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1042 LYS Chi-restraints excluded: chain A residue 1062 SER Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1104 ASP Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1299 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [118, 38, 50, 62, 124, 33, 67, 22, 43, 92, 51] chunk 118 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1189 GLN A1228 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.107249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.084761 restraints weight = 15719.878| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.57 r_work: 0.2875 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10445 Z= 0.226 Angle : 0.564 8.991 14168 Z= 0.289 Chirality : 0.044 0.246 1531 Planarity : 0.004 0.044 1806 Dihedral : 6.168 87.688 1413 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.38 % Favored : 97.54 % Rotamer: Outliers : 2.68 % Allowed : 11.44 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.33 (0.24), residues: 1261 helix: 1.74 (0.19), residues: 695 sheet: -0.55 (0.49), residues: 104 loop : 0.02 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 911 TYR 0.020 0.002 TYR A1101 PHE 0.023 0.002 PHE A1428 TRP 0.009 0.001 TRP A 634 HIS 0.003 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 (10442) covalent geometry : angle 0.56344 / 0.29 (14162) SS BOND : bond 0.00289 / 0.14 ( 3) SS BOND : angle 1.20388 / 0.51 ( 6) hydrogen bonds : bond 0.04250 / 2.83 ( 566) hydrogen bonds : angle 4.26829 / 3.00 ( 1644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 298 ASP cc_start: 0.8239 (p0) cc_final: 0.7816 (p0) REVERT: A 299 PHE cc_start: 0.8492 (m-80) cc_final: 0.8270 (m-10) REVERT: A 564 GLU cc_start: 0.7601 (pt0) cc_final: 0.7331 (pt0) REVERT: A 567 SER cc_start: 0.8818 (m) cc_final: 0.8472 (p) REVERT: A 570 GLU cc_start: 0.8930 (tt0) cc_final: 0.8616 (tm-30) REVERT: A 657 MET cc_start: 0.8359 (mmm) cc_final: 0.7864 (mpp) REVERT: A 670 TYR cc_start: 0.9278 (m-80) cc_final: 0.9074 (m-80) REVERT: A 742 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: A 894 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.9105 (ttm) REVERT: A 1042 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8462 (mmtt) REVERT: A 1109 GLU cc_start: 0.8628 (pm20) cc_final: 0.8427 (pm20) REVERT: A 1299 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8630 (mp) REVERT: A 1341 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8573 (tm-30) outliers start: 29 outliers final: 17 residues processed: 114 average time/residue: 0.5239 time to fit residues: 64.7995 Evaluate side-chains 113 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain A residue 921 GLU Chi-restraints excluded: chain A residue 1042 LYS Chi-restraints excluded: chain A residue 1062 SER Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1341 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [75, 107, 87, 17, 125, 30, 114, 120, 122, 111, 39] chunk 75 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 404 GLN A 724 ASN A1189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.108825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.086378 restraints weight = 15486.432| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.57 r_work: 0.2901 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10445 Z= 0.148 Angle : 0.522 9.251 14168 Z= 0.267 Chirality : 0.042 0.257 1531 Planarity : 0.004 0.042 1806 Dihedral : 6.202 86.401 1413 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.14 % Favored : 97.78 % Rotamer: Outliers : 2.31 % Allowed : 11.99 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.45 (0.24), residues: 1261 helix: 1.86 (0.19), residues: 695 sheet: -0.57 (0.49), residues: 104 loop : 0.06 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 230 TYR 0.014 0.001 TYR A1297 PHE 0.018 0.001 PHE A 552 TRP 0.011 0.001 TRP A 634 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (10442) covalent geometry : angle 0.52147 / 0.27 (14162) SS BOND : bond 0.00204 / 0.10 ( 3) SS BOND : angle 0.97796 / 0.42 ( 6) hydrogen bonds : bond 0.03872 / 2.56 ( 566) hydrogen bonds : angle 4.17179 / 2.93 ( 1644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.336 Fit side-chains REVERT: A 227 ARG cc_start: 0.8500 (ttp-170) cc_final: 0.8106 (ptp-110) REVERT: A 298 ASP cc_start: 0.8308 (p0) cc_final: 0.7926 (p0) REVERT: A 299 PHE cc_start: 0.8464 (m-80) cc_final: 0.8251 (m-10) REVERT: A 439 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6946 (tm-30) REVERT: A 564 GLU cc_start: 0.7409 (pt0) cc_final: 0.7201 (pt0) REVERT: A 567 SER cc_start: 0.8770 (m) cc_final: 0.8477 (p) REVERT: A 570 GLU cc_start: 0.8945 (tt0) cc_final: 0.8618 (tm-30) REVERT: A 657 MET cc_start: 0.8348 (mmm) cc_final: 0.7863 (mpp) REVERT: A 742 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: A 894 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.8913 (ttm) REVERT: A 1042 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8356 (mmtt) REVERT: A 1299 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8589 (mp) REVERT: A 1341 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8541 (tm-30) outliers start: 25 outliers final: 14 residues processed: 113 average time/residue: 0.5193 time to fit residues: 63.6443 Evaluate side-chains 113 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain A residue 921 GLU Chi-restraints excluded: chain A residue 1042 LYS Chi-restraints excluded: chain A residue 1062 SER Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1341 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [63, 41, 22, 27, 94, 12, 48, 11, 6, 114, 56] chunk 63 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.108698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.086271 restraints weight = 15518.022| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.57 r_work: 0.2899 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10445 Z= 0.155 Angle : 0.527 9.401 14168 Z= 0.269 Chirality : 0.042 0.275 1531 Planarity : 0.004 0.042 1806 Dihedral : 6.169 84.153 1413 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.98 % Favored : 97.94 % Rotamer: Outliers : 2.49 % Allowed : 11.62 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.46 (0.24), residues: 1261 helix: 1.88 (0.19), residues: 696 sheet: -0.62 (0.49), residues: 104 loop : 0.04 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 230 TYR 0.014 0.001 TYR A1297 PHE 0.020 0.001 PHE A 552 TRP 0.010 0.001 TRP A 634 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (10442) covalent geometry : angle 0.52711 / 0.27 (14162) SS BOND : bond 0.00213 / 0.10 ( 3) SS BOND : angle 0.97968 / 0.42 ( 6) hydrogen bonds : bond 0.03856 / 2.55 ( 566) hydrogen bonds : angle 4.14616 / 2.91 ( 1644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.298 Fit side-chains REVERT: A 227 ARG cc_start: 0.8499 (ttp-170) cc_final: 0.7897 (ptp-170) REVERT: A 298 ASP cc_start: 0.8358 (p0) cc_final: 0.8074 (p0) REVERT: A 307 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: A 439 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: A 567 SER cc_start: 0.8763 (m) cc_final: 0.8443 (p) REVERT: A 657 MET cc_start: 0.8355 (mmm) cc_final: 0.7778 (mpp) REVERT: A 742 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: A 894 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8917 (ttm) REVERT: A 1042 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8374 (mmtt) REVERT: A 1299 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8600 (mp) outliers start: 27 outliers final: 16 residues processed: 111 average time/residue: 0.5090 time to fit residues: 61.3693 Evaluate side-chains 115 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain A residue 921 GLU Chi-restraints excluded: chain A residue 1042 LYS Chi-restraints excluded: chain A residue 1062 SER Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1311 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [9, 103, 70, 86, 41, 106, 112, 16, 100, 85, 40] chunk 9 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.108130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.085847 restraints weight = 15489.550| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.55 r_work: 0.2893 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10445 Z= 0.167 Angle : 0.524 9.246 14168 Z= 0.269 Chirality : 0.043 0.331 1531 Planarity : 0.004 0.042 1806 Dihedral : 6.140 82.663 1413 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.98 % Favored : 97.94 % Rotamer: Outliers : 2.49 % Allowed : 11.99 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.48 (0.24), residues: 1261 helix: 1.89 (0.19), residues: 697 sheet: -0.64 (0.49), residues: 104 loop : 0.07 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 911 TYR 0.014 0.001 TYR A1297 PHE 0.020 0.002 PHE A 552 TRP 0.010 0.001 TRP A 634 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (10442) covalent geometry : angle 0.52352 / 0.27 (14162) SS BOND : bond 0.00231 / 0.11 ( 3) SS BOND : angle 0.99537 / 0.42 ( 6) hydrogen bonds : bond 0.03904 / 2.58 ( 566) hydrogen bonds : angle 4.14907 / 2.91 ( 1644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8682 (mmtm) cc_final: 0.8338 (mppt) REVERT: A 298 ASP cc_start: 0.8275 (p0) cc_final: 0.7947 (p0) REVERT: A 299 PHE cc_start: 0.8459 (m-80) cc_final: 0.8105 (m-10) REVERT: A 307 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: A 439 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6927 (tm-30) REVERT: A 525 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8201 (mmm) REVERT: A 567 SER cc_start: 0.8656 (m) cc_final: 0.8380 (p) REVERT: A 657 MET cc_start: 0.8369 (mmm) cc_final: 0.7789 (mpp) REVERT: A 742 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: A 894 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8915 (ttm) REVERT: A 1042 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8433 (mmtt) REVERT: A 1299 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8602 (mp) outliers start: 27 outliers final: 17 residues processed: 111 average time/residue: 0.5302 time to fit residues: 64.0387 Evaluate side-chains 115 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain A residue 921 GLU Chi-restraints excluded: chain A residue 1042 LYS Chi-restraints excluded: chain A residue 1062 SER Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [8, 52, 120, 98, 115, 75, 74, 22, 113, 56, 108] chunk 8 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1189 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.086362 restraints weight = 15332.898| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.56 r_work: 0.2898 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10445 Z= 0.151 Angle : 0.526 10.557 14168 Z= 0.268 Chirality : 0.042 0.326 1531 Planarity : 0.004 0.041 1806 Dihedral : 6.107 81.697 1413 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.14 % Favored : 97.78 % Rotamer: Outliers : 2.49 % Allowed : 11.99 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.51 (0.24), residues: 1261 helix: 1.92 (0.19), residues: 697 sheet: -0.67 (0.48), residues: 104 loop : 0.09 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 572 TYR 0.013 0.001 TYR A1297 PHE 0.019 0.001 PHE A1428 TRP 0.011 0.001 TRP A 634 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (10442) covalent geometry : angle 0.52568 / 0.27 (14162) SS BOND : bond 0.00217 / 0.10 ( 3) SS BOND : angle 0.94606 / 0.40 ( 6) hydrogen bonds : bond 0.03802 / 2.52 ( 566) hydrogen bonds : angle 4.12666 / 2.90 ( 1644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8693 (mmtm) cc_final: 0.8325 (mppt) REVERT: A 227 ARG cc_start: 0.8495 (ttp-170) cc_final: 0.8098 (ptp-110) REVERT: A 298 ASP cc_start: 0.8306 (p0) cc_final: 0.7973 (p0) REVERT: A 299 PHE cc_start: 0.8467 (m-80) cc_final: 0.8114 (m-10) REVERT: A 307 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7912 (tt0) REVERT: A 381 TYR cc_start: 0.8595 (m-80) cc_final: 0.7318 (m-80) REVERT: A 567 SER cc_start: 0.8602 (m) cc_final: 0.8334 (p) REVERT: A 657 MET cc_start: 0.8365 (mmm) cc_final: 0.7794 (mpp) REVERT: A 742 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: A 894 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8894 (ttm) REVERT: A 999 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7511 (pp20) REVERT: A 1042 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8434 (mmtt) REVERT: A 1299 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8625 (mp) outliers start: 27 outliers final: 17 residues processed: 114 average time/residue: 0.4918 time to fit residues: 61.3420 Evaluate side-chains 116 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain A residue 921 GLU Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1042 LYS Chi-restraints excluded: chain A residue 1062 SER Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: [117, 70, 99, 116, 36, 89, 59, 76, 0, 81, 102] chunk 117 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 99 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 102 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3392 r_free = 0.3392 target = 0.109494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.087153 restraints weight = 15564.196| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.58 r_work: 0.2920 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10445 Z= 0.130 Angle : 0.514 9.202 14168 Z= 0.261 Chirality : 0.042 0.330 1531 Planarity : 0.004 0.042 1806 Dihedral : 6.016 79.670 1413 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.14 % Favored : 97.78 % Rotamer: Outliers : 2.21 % Allowed : 12.55 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.66 (0.24), residues: 1261 helix: 2.05 (0.19), residues: 692 sheet: -0.66 (0.49), residues: 104 loop : 0.18 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 572 TYR 0.012 0.001 TYR A1297 PHE 0.020 0.001 PHE A1428 TRP 0.012 0.001 TRP A 634 HIS 0.002 0.000 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10442) covalent geometry : angle 0.51408 / 0.26 (14162) SS BOND : bond 0.00178 / 0.09 ( 3) SS BOND : angle 0.88185 / 0.38 ( 6) hydrogen bonds : bond 0.03650 / 2.41 ( 566) hydrogen bonds : angle 4.07258 / 2.86 ( 1644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3159.81 seconds wall clock time: 54 minutes 41.41 seconds (3281.41 seconds total)