Starting phenix.real_space_refine on Thu Mar 5 14:39:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b2q_11990/03_2026/7b2q_11990_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b2q_11990/03_2026/7b2q_11990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b2q_11990/03_2026/7b2q_11990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b2q_11990/03_2026/7b2q_11990.map" model { file = "/net/cci-nas-00/data/ceres_data/7b2q_11990/03_2026/7b2q_11990_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b2q_11990/03_2026/7b2q_11990_trim.cif" } resolution = 3.76 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 44 5.16 5 C 7355 2.51 5 N 2007 2.21 5 O 2205 1.98 5 H 11430 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23041 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 10007 Classifications: {'peptide': 650} Link IDs: {'PCIS': 3, 'PTRANS': 41, 'TRANS': 605} Chain: "B" Number of atoms: 9222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 9222 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 27, 'TRANS': 572} Chain breaks: 6 Chain: "C" Number of atoms: 1958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1958 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "D" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1784 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.75, per 1000 atoms: 0.16 Number of scatterers: 23041 At special positions: 0 Unit cell: (135.762, 122.391, 131.648, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 O 2205 8.00 N 2007 7.00 C 7355 6.00 H 11430 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS B 820 " distance=2.04 Simple disulfide: pdb=" SG CYS A 635 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 876 " - pdb=" SG CYS C1590 " distance=2.03 Simple disulfide: pdb=" SG CYS B1394 " - pdb=" SG CYS C1566 " distance=2.03 Simple disulfide: pdb=" SG CYS C1471 " - pdb=" SG CYS C1535 " distance=2.04 Simple disulfide: pdb=" SG CYS C1583 " - pdb=" SG CYS C1588 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B1801 " - " ASN B 862 " " NAG B1802 " - " ASN B1328 " " NAG B1803 " - " ASN B1391 " " NAG E 1 " - " ASN A 226 " Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 729.1 milliseconds 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2762 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 28 sheets defined 19.5% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.762A pdb=" N ARG A 63 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 97 removed outlier: 3.706A pdb=" N ALA A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 315 through 327 Processing helix chain 'A' and resid 606 through 611 removed outlier: 3.771A pdb=" N ALA A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 642 through 650 Processing helix chain 'B' and resid 999 through 1004 Processing helix chain 'B' and resid 1012 through 1017 removed outlier: 3.807A pdb=" N ILE B1016 " --> pdb=" O GLU B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1032 Processing helix chain 'B' and resid 1038 through 1058 removed outlier: 3.855A pdb=" N LYS B1042 " --> pdb=" O PRO B1038 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP B1043 " --> pdb=" O PRO B1039 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP B1047 " --> pdb=" O ASP B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1090 Processing helix chain 'B' and resid 1096 through 1110 removed outlier: 3.568A pdb=" N LEU B1100 " --> pdb=" O SER B1096 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR B1103 " --> pdb=" O LYS B1099 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B1107 " --> pdb=" O THR B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1130 removed outlier: 4.012A pdb=" N MET B1128 " --> pdb=" O ASP B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1156 removed outlier: 3.701A pdb=" N LEU B1153 " --> pdb=" O LEU B1149 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B1154 " --> pdb=" O HIS B1150 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL B1155 " --> pdb=" O HIS B1151 " (cutoff:3.500A) Processing helix chain 'B' and resid 1161 through 1186 removed outlier: 3.563A pdb=" N ARG B1167 " --> pdb=" O PRO B1163 " (cutoff:3.500A) Processing helix chain 'B' and resid 1189 through 1203 Processing helix chain 'B' and resid 1206 through 1221 removed outlier: 3.561A pdb=" N ALA B1219 " --> pdb=" O ASN B1215 " (cutoff:3.500A) Processing helix chain 'B' and resid 1258 through 1275 Processing helix chain 'B' and resid 1281 through 1294 removed outlier: 3.726A pdb=" N ALA B1287 " --> pdb=" O ASP B1283 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TRP B1288 " --> pdb=" O GLN B1284 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B1291 " --> pdb=" O ALA B1287 " (cutoff:3.500A) Processing helix chain 'B' and resid 1302 through 1320 Processing helix chain 'C' and resid 1497 through 1507 removed outlier: 3.641A pdb=" N LEU C1507 " --> pdb=" O LYS C1503 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 61 removed outlier: 3.669A pdb=" N LYS D 61 " --> pdb=" O PRO D 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 58 through 61' Processing helix chain 'D' and resid 83 through 87 removed outlier: 4.253A pdb=" N THR D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 87 removed outlier: 7.823A pdb=" N SER A 38 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.097A pdb=" N VAL A 31 " --> pdb=" O SER A 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 52 Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 145 Processing sheet with id=AA5, first strand: chain 'A' and resid 149 through 150 Processing sheet with id=AA6, first strand: chain 'A' and resid 185 through 192 removed outlier: 3.584A pdb=" N ARG A 187 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A 218 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 214 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 241 through 247 removed outlier: 3.514A pdb=" N ARG A 269 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET A 262 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 252 through 253 removed outlier: 5.154A pdb=" N ILE A 252 " --> pdb=" O VAL A 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 279 through 280 Processing sheet with id=AB1, first strand: chain 'A' and resid 293 through 295 Processing sheet with id=AB2, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.715A pdb=" N LEU A 386 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 433 " --> pdb=" O LEU A 386 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 417 through 423 removed outlier: 3.521A pdb=" N GLU A 443 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 448 " --> pdb=" O ALA A 458 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 450 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 488 through 493 removed outlier: 4.294A pdb=" N THR A 527 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 515 through 522 removed outlier: 3.595A pdb=" N PHE A 517 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N HIS A 504 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N TYR A 548 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 510 " --> pdb=" O TYR A 542 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N HIS A 552 " --> pdb=" O HIS A 549 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 515 through 522 removed outlier: 3.595A pdb=" N PHE A 517 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N HIS A 504 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N TYR A 548 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 510 " --> pdb=" O TYR A 542 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 572 through 574 removed outlier: 3.922A pdb=" N LEU B 795 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 787 through 788 removed outlier: 3.840A pdb=" N SER B 812 " --> pdb=" O CYS B 820 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS B 820 " --> pdb=" O SER B 812 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 804 through 808 Processing sheet with id=AC1, first strand: chain 'B' and resid 833 through 836 removed outlier: 3.515A pdb=" N HIS B 836 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN B 857 " --> pdb=" O SER B 893 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 885 through 889 removed outlier: 3.771A pdb=" N VAL B 867 " --> pdb=" O GLN B 885 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS B 868 " --> pdb=" O VAL B 914 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 914 " --> pdb=" O HIS B 868 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 911 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 929 " --> pdb=" O LEU B 911 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 875 through 876 removed outlier: 3.572A pdb=" N CYS B 876 " --> pdb=" O VAL B 902 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 902 " --> pdb=" O CYS B 876 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 939 through 945 removed outlier: 3.554A pdb=" N LEU B 944 " --> pdb=" O VAL B1380 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B1380 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 959 through 960 removed outlier: 3.776A pdb=" N ILE B 960 " --> pdb=" O ILE B1366 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B1366 " --> pdb=" O ILE B 960 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B1329 " --> pdb=" O LEU B1344 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1397 through 1401 removed outlier: 3.572A pdb=" N TRP C1473 " --> pdb=" O GLN B1398 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1404 through 1405 removed outlier: 3.504A pdb=" N LYS B1404 " --> pdb=" O HIS C1467 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C1541 " --> pdb=" O HIS C1495 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1512 through 1518 removed outlier: 3.752A pdb=" N HIS C1514 " --> pdb=" O TYR C1525 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C1524 " --> pdb=" O ALA C1486 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.515A pdb=" N SER D 7 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR D 74 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP D 69 " --> pdb=" O THR D 74 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR D 65 " --> pdb=" O GLN D 78 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 54 through 56 removed outlier: 7.117A pdb=" N TRP D 32 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA D 88 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL D 116 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR D 90 " --> pdb=" O THR D 114 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1122 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: 6.04 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11428 1.03 - 1.23: 263 1.23 - 1.43: 4686 1.43 - 1.63: 6841 1.63 - 1.82: 70 Bond restraints: 23288 Sorted by residual: bond pdb=" C1 NAG B1801 " pdb=" O5 NAG B1801 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C1 NAG B1803 " pdb=" O5 NAG B1803 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.59e+00 bond pdb=" N THR C1469 " pdb=" CA THR C1469 " ideal model delta sigma weight residual 1.465 1.449 0.016 1.31e-02 5.83e+03 1.58e+00 bond pdb=" C GLU A 346 " pdb=" N SER A 347 " ideal model delta sigma weight residual 1.329 1.309 0.019 1.60e-02 3.91e+03 1.47e+00 ... (remaining 23283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 40071 1.13 - 2.27: 1823 2.27 - 3.40: 140 3.40 - 4.53: 37 4.53 - 5.67: 2 Bond angle restraints: 42073 Sorted by residual: angle pdb=" N VAL A 186 " pdb=" CA VAL A 186 " pdb=" C VAL A 186 " ideal model delta sigma weight residual 113.71 111.02 2.69 9.50e-01 1.11e+00 8.01e+00 angle pdb=" CA CYS A 567 " pdb=" CB CYS A 567 " pdb=" SG CYS A 567 " ideal model delta sigma weight residual 114.40 120.07 -5.67 2.30e+00 1.89e-01 6.07e+00 angle pdb=" N PHE B 846 " pdb=" CA PHE B 846 " pdb=" C PHE B 846 " ideal model delta sigma weight residual 113.56 110.47 3.09 1.39e+00 5.18e-01 4.93e+00 angle pdb=" CA LYS D 83 " pdb=" CB LYS D 83 " pdb=" CG LYS D 83 " ideal model delta sigma weight residual 114.10 118.41 -4.31 2.00e+00 2.50e-01 4.64e+00 angle pdb=" N GLU A 568 " pdb=" CA GLU A 568 " pdb=" C GLU A 568 " ideal model delta sigma weight residual 113.97 111.24 2.73 1.28e+00 6.10e-01 4.54e+00 ... (remaining 42068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 9941 17.22 - 34.43: 821 34.43 - 51.65: 235 51.65 - 68.87: 61 68.87 - 86.09: 13 Dihedral angle restraints: 11071 sinusoidal: 6116 harmonic: 4955 Sorted by residual: dihedral pdb=" CB CYS A 635 " pdb=" SG CYS A 635 " pdb=" SG CYS A 669 " pdb=" CB CYS A 669 " ideal model delta sinusoidal sigma weight residual 93.00 167.55 -74.55 1 1.00e+01 1.00e-02 7.04e+01 dihedral pdb=" CB CYS C1471 " pdb=" SG CYS C1471 " pdb=" SG CYS C1535 " pdb=" CB CYS C1535 " ideal model delta sinusoidal sigma weight residual 93.00 48.23 44.77 1 1.00e+01 1.00e-02 2.78e+01 dihedral pdb=" CA LYS D 83 " pdb=" C LYS D 83 " pdb=" N PRO D 84 " pdb=" CA PRO D 84 " ideal model delta harmonic sigma weight residual 180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 11068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1518 0.049 - 0.098: 220 0.098 - 0.147: 94 0.147 - 0.196: 2 0.196 - 0.245: 1 Chirality restraints: 1835 Sorted by residual: chirality pdb=" C1 NAG B1802 " pdb=" ND2 ASN B1328 " pdb=" C2 NAG B1802 " pdb=" O5 NAG B1802 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" C1 NAG B1803 " pdb=" ND2 ASN B1391 " pdb=" C2 NAG B1803 " pdb=" O5 NAG B1803 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CA PRO D 84 " pdb=" N PRO D 84 " pdb=" C PRO D 84 " pdb=" CB PRO D 84 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 1832 not shown) Planarity restraints: 3485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 636 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO A 637 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 637 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 637 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B1121 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO B1122 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B1122 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B1122 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 46 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO A 47 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 47 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 47 " -0.019 5.00e-02 4.00e+02 ... (remaining 3482 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 627 2.11 - 2.74: 41664 2.74 - 3.36: 63556 3.36 - 3.98: 81668 3.98 - 4.60: 127477 Nonbonded interactions: 314992 Sorted by model distance: nonbonded pdb=" O GLN B1395 " pdb="HD21 ASN C1475 " model vdw 1.493 2.450 nonbonded pdb=" O MET B 841 " pdb="HE22 GLN B 932 " model vdw 1.497 2.450 nonbonded pdb="HH21 ARG A 22 " pdb=" OD2 ASP A 658 " model vdw 1.517 2.450 nonbonded pdb=" HG1 THR A 606 " pdb=" O THR B 805 " model vdw 1.555 2.450 nonbonded pdb="HH22 ARG A 138 " pdb=" OD2 ASP A 172 " model vdw 1.560 2.450 ... (remaining 314987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.890 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: 0.130 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.580 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 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 : 0.004 0.036 11871 Z= 0.171 Angle : 0.557 8.738 16128 Z= 0.297 Chirality : 0.042 0.245 1835 Planarity : 0.003 0.057 2077 Dihedral : 13.626 86.086 4413 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.23 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -0.98 (0.22), residues: 1473 helix: 0.39 (0.34), residues: 262 sheet: -0.76 (0.24), residues: 485 loop : -0.86 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 103 TYR 0.015 0.001 TYR D 29 PHE 0.008 0.001 PHE A 82 TRP 0.006 0.001 TRP A 360 HIS 0.004 0.001 HIS B1150 Details of bonding type rmsd covalent geometry : bond 0.00359 (11858) covalent geometry : angle 0.54698 (16097) SS BOND : bond 0.00336 ( 8) SS BOND : angle 1.79180 ( 16) hydrogen bonds : bond 0.28892 ( 406) hydrogen bonds : angle 9.90954 ( 1122) link_BETA1-4 : bond 0.00147 ( 1) link_BETA1-4 : angle 1.07865 ( 3) link_NAG-ASN : bond 0.00553 ( 4) link_NAG-ASN : angle 3.37514 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7117 (pp30) cc_final: 0.6796 (pp30) REVERT: A 53 LYS cc_start: 0.7713 (ptpp) cc_final: 0.7479 (ptpt) REVERT: A 57 PHE cc_start: 0.5973 (p90) cc_final: 0.5737 (p90) REVERT: A 124 THR cc_start: 0.7998 (p) cc_final: 0.7773 (t) REVERT: A 166 LYS cc_start: 0.8042 (mtmm) cc_final: 0.7819 (mtmm) REVERT: A 179 GLU cc_start: 0.7175 (tt0) cc_final: 0.6960 (tt0) REVERT: A 209 GLU cc_start: 0.7285 (mm-30) cc_final: 0.7061 (mm-30) REVERT: A 328 MET cc_start: 0.6674 (tpp) cc_final: 0.5525 (tpp) REVERT: A 378 LEU cc_start: 0.7920 (pt) cc_final: 0.7687 (pp) REVERT: A 404 LYS cc_start: 0.7143 (mttp) cc_final: 0.6847 (mtmt) REVERT: A 419 GLN cc_start: 0.7231 (tt0) cc_final: 0.6945 (tm-30) REVERT: A 523 LYS cc_start: 0.7499 (ttpt) cc_final: 0.7147 (ttpp) REVERT: A 558 LEU cc_start: 0.8586 (tp) cc_final: 0.8321 (tp) REVERT: A 632 ASP cc_start: 0.7808 (t0) cc_final: 0.7569 (t0) REVERT: A 658 ASP cc_start: 0.7207 (m-30) cc_final: 0.6967 (m-30) REVERT: B 817 LYS cc_start: 0.7618 (mmtt) cc_final: 0.7045 (mmmm) REVERT: B 833 PHE cc_start: 0.7406 (t80) cc_final: 0.7134 (t80) REVERT: B 857 ASN cc_start: 0.7403 (t0) cc_final: 0.7201 (t0) REVERT: B 866 SER cc_start: 0.8534 (t) cc_final: 0.8278 (p) REVERT: B 942 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6833 (mt-10) REVERT: B 1029 ASP cc_start: 0.7462 (t0) cc_final: 0.7171 (m-30) REVERT: B 1084 LYS cc_start: 0.8339 (ttmt) cc_final: 0.7978 (ttmm) REVERT: B 1288 TRP cc_start: 0.7739 (t60) cc_final: 0.7469 (t-100) REVERT: B 1317 ILE cc_start: 0.8282 (pt) cc_final: 0.7312 (mt) REVERT: B 1388 ASP cc_start: 0.6950 (p0) cc_final: 0.6719 (p0) REVERT: B 1389 MET cc_start: 0.5744 (pmm) cc_final: 0.5216 (pmm) REVERT: B 1411 MET cc_start: 0.6819 (ppp) cc_final: 0.6005 (ppp) REVERT: D 27 ARG cc_start: 0.6611 (ttt90) cc_final: 0.6277 (ttt-90) REVERT: D 28 THR cc_start: 0.5700 (t) cc_final: 0.5472 (t) REVERT: D 63 ARG cc_start: 0.8273 (ttp80) cc_final: 0.7878 (ttp80) REVERT: D 104 VAL cc_start: 0.7049 (m) cc_final: 0.6846 (m) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.2804 time to fit residues: 134.4660 Evaluate side-chains 326 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0470 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN B 848 GLN B1216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.132920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.112462 restraints weight = 56366.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.117946 restraints weight = 21570.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.121340 restraints weight = 10892.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.123304 restraints weight = 6649.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.124760 restraints weight = 4772.107| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11871 Z= 0.151 Angle : 0.600 8.506 16128 Z= 0.317 Chirality : 0.044 0.281 1835 Planarity : 0.005 0.041 2077 Dihedral : 5.423 51.446 1715 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.71 % Allowed : 8.82 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -0.91 (0.22), residues: 1473 helix: 0.45 (0.31), residues: 263 sheet: -0.67 (0.24), residues: 491 loop : -0.86 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 269 TYR 0.010 0.001 TYR A 507 PHE 0.020 0.001 PHE A 319 TRP 0.010 0.001 TRP D 32 HIS 0.005 0.001 HIS B1150 Details of bonding type rmsd covalent geometry : bond 0.00322 (11858) covalent geometry : angle 0.59129 (16097) SS BOND : bond 0.00532 ( 8) SS BOND : angle 1.74044 ( 16) hydrogen bonds : bond 0.06834 ( 406) hydrogen bonds : angle 7.22448 ( 1122) link_BETA1-4 : bond 0.00012 ( 1) link_BETA1-4 : angle 1.03881 ( 3) link_NAG-ASN : bond 0.00612 ( 4) link_NAG-ASN : angle 3.34191 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 323 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7374 (pp30) cc_final: 0.6936 (pp30) REVERT: A 53 LYS cc_start: 0.7780 (ptpp) cc_final: 0.7511 (ptpt) REVERT: A 57 PHE cc_start: 0.5764 (p90) cc_final: 0.5547 (p90) REVERT: A 107 GLU cc_start: 0.6415 (mp0) cc_final: 0.6210 (mp0) REVERT: A 231 PHE cc_start: 0.8385 (p90) cc_final: 0.8114 (p90) REVERT: A 269 ARG cc_start: 0.6959 (mmm160) cc_final: 0.6403 (mtm180) REVERT: A 328 MET cc_start: 0.6280 (tpp) cc_final: 0.5805 (tpp) REVERT: A 346 GLU cc_start: 0.6850 (tm-30) cc_final: 0.6565 (tm-30) REVERT: A 363 VAL cc_start: 0.7245 (m) cc_final: 0.7031 (p) REVERT: A 404 LYS cc_start: 0.7491 (mttp) cc_final: 0.7170 (mtmt) REVERT: A 523 LYS cc_start: 0.7502 (ttpt) cc_final: 0.7217 (ttpp) REVERT: A 558 LEU cc_start: 0.8629 (tp) cc_final: 0.8303 (tp) REVERT: A 570 LYS cc_start: 0.7232 (tmmt) cc_final: 0.6972 (tmmt) REVERT: A 632 ASP cc_start: 0.7835 (t0) cc_final: 0.7565 (t0) REVERT: B 808 ILE cc_start: 0.6323 (mt) cc_final: 0.6030 (mt) REVERT: B 817 LYS cc_start: 0.7599 (mmtt) cc_final: 0.7353 (mmtt) REVERT: B 841 MET cc_start: 0.3760 (pmm) cc_final: 0.3557 (pmm) REVERT: B 857 ASN cc_start: 0.7386 (t0) cc_final: 0.7021 (t0) REVERT: B 934 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7022 (mm-30) REVERT: B 936 GLU cc_start: 0.7140 (mp0) cc_final: 0.6921 (mp0) REVERT: B 942 GLU cc_start: 0.6793 (mt-10) cc_final: 0.6379 (mt-10) REVERT: B 1029 ASP cc_start: 0.7566 (t0) cc_final: 0.7296 (m-30) REVERT: B 1288 TRP cc_start: 0.7663 (t60) cc_final: 0.7323 (t-100) REVERT: B 1369 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8405 (mtpp) REVERT: B 1389 MET cc_start: 0.5914 (pmm) cc_final: 0.5487 (pmm) REVERT: C 1523 LEU cc_start: 0.7690 (mp) cc_final: 0.7477 (mp) REVERT: D 27 ARG cc_start: 0.6483 (ttt90) cc_final: 0.6281 (ttt-90) REVERT: D 28 THR cc_start: 0.5249 (t) cc_final: 0.4999 (t) REVERT: D 63 ARG cc_start: 0.8300 (ttp80) cc_final: 0.7893 (ttp80) outliers start: 9 outliers final: 4 residues processed: 325 average time/residue: 0.2611 time to fit residues: 116.2002 Evaluate side-chains 309 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 305 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 1203 THR Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1301 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 146 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 GLN ** B1129 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 = 0.3748 r_free = 0.3748 target = 0.130029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.109710 restraints weight = 56545.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.115043 restraints weight = 21783.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.118322 restraints weight = 11093.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.120328 restraints weight = 6851.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.121674 restraints weight = 4900.105| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11871 Z= 0.222 Angle : 0.612 8.134 16128 Z= 0.321 Chirality : 0.044 0.283 1835 Planarity : 0.005 0.049 2077 Dihedral : 5.200 50.155 1715 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.51 % Allowed : 10.88 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -1.24 (0.21), residues: 1473 helix: 0.15 (0.31), residues: 266 sheet: -0.89 (0.23), residues: 500 loop : -1.05 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 337 TYR 0.018 0.002 TYR A 507 PHE 0.025 0.002 PHE A 319 TRP 0.012 0.002 TRP B 782 HIS 0.007 0.001 HIS B1342 Details of bonding type rmsd covalent geometry : bond 0.00478 (11858) covalent geometry : angle 0.60230 (16097) SS BOND : bond 0.00251 ( 8) SS BOND : angle 1.94146 ( 16) hydrogen bonds : bond 0.05519 ( 406) hydrogen bonds : angle 6.52371 ( 1122) link_BETA1-4 : bond 0.00353 ( 1) link_BETA1-4 : angle 1.71932 ( 3) link_NAG-ASN : bond 0.00677 ( 4) link_NAG-ASN : angle 3.22967 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 322 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7386 (pp30) cc_final: 0.6818 (pp30) REVERT: A 53 LYS cc_start: 0.7830 (ptpp) cc_final: 0.7570 (ptpt) REVERT: A 57 PHE cc_start: 0.5825 (p90) cc_final: 0.5616 (p90) REVERT: A 166 LYS cc_start: 0.8042 (mtmm) cc_final: 0.7680 (mtmm) REVERT: A 231 PHE cc_start: 0.8534 (p90) cc_final: 0.8242 (p90) REVERT: A 234 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7432 (ptmt) REVERT: A 328 MET cc_start: 0.6230 (tpp) cc_final: 0.5760 (tpp) REVERT: A 346 GLU cc_start: 0.6827 (tm-30) cc_final: 0.6492 (tm-30) REVERT: A 378 LEU cc_start: 0.7929 (pt) cc_final: 0.7719 (pp) REVERT: A 404 LYS cc_start: 0.7708 (mttp) cc_final: 0.7377 (mtmt) REVERT: A 523 LYS cc_start: 0.7605 (ttpt) cc_final: 0.7194 (ttpp) REVERT: A 570 LYS cc_start: 0.7175 (tmmt) cc_final: 0.6922 (tmmt) REVERT: A 632 ASP cc_start: 0.7812 (t0) cc_final: 0.7578 (t0) REVERT: A 659 GLN cc_start: 0.8090 (mt0) cc_final: 0.7727 (mt0) REVERT: A 660 TRP cc_start: 0.7629 (p-90) cc_final: 0.6254 (p90) REVERT: B 817 LYS cc_start: 0.7712 (mmtt) cc_final: 0.7453 (mmtt) REVERT: B 841 MET cc_start: 0.3976 (pmm) cc_final: 0.3726 (pmm) REVERT: B 857 ASN cc_start: 0.7642 (t0) cc_final: 0.7229 (t0) REVERT: B 934 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7047 (mm-30) REVERT: B 1100 LEU cc_start: 0.7718 (mt) cc_final: 0.7491 (mm) REVERT: B 1222 GLN cc_start: 0.6425 (tm-30) cc_final: 0.6182 (mm110) REVERT: B 1288 TRP cc_start: 0.7792 (t60) cc_final: 0.7552 (t-100) REVERT: B 1369 LYS cc_start: 0.8651 (mtpt) cc_final: 0.8372 (mtpp) REVERT: B 1389 MET cc_start: 0.5911 (pmm) cc_final: 0.5609 (pmm) REVERT: C 1510 ARG cc_start: 0.6656 (ptm-80) cc_final: 0.6377 (ptm-80) REVERT: D 27 ARG cc_start: 0.6544 (ttt90) cc_final: 0.6257 (ttt180) REVERT: D 28 THR cc_start: 0.5397 (t) cc_final: 0.5185 (t) REVERT: D 53 MET cc_start: 0.4929 (mtm) cc_final: 0.4691 (mtm) REVERT: D 55 GLU cc_start: 0.4800 (pp20) cc_final: 0.3997 (pp20) outliers start: 19 outliers final: 10 residues processed: 327 average time/residue: 0.2539 time to fit residues: 114.7010 Evaluate side-chains 324 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 313 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain B residue 1149 LEU Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1301 SER Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain C residue 1466 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 122 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 124 optimal weight: 0.0870 chunk 48 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.131210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.110752 restraints weight = 55987.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.116169 restraints weight = 21461.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.119460 restraints weight = 10897.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.121608 restraints weight = 6754.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.122789 restraints weight = 4758.412| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11871 Z= 0.144 Angle : 0.568 8.287 16128 Z= 0.294 Chirality : 0.043 0.258 1835 Planarity : 0.004 0.044 2077 Dihedral : 4.898 47.683 1715 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.75 % Allowed : 12.87 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -1.13 (0.22), residues: 1473 helix: 0.36 (0.31), residues: 266 sheet: -0.87 (0.24), residues: 488 loop : -0.98 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1026 TYR 0.012 0.001 TYR B1198 PHE 0.018 0.001 PHE D 33 TRP 0.008 0.001 TRP D 32 HIS 0.004 0.001 HIS B1150 Details of bonding type rmsd covalent geometry : bond 0.00316 (11858) covalent geometry : angle 0.55910 (16097) SS BOND : bond 0.00527 ( 8) SS BOND : angle 1.52079 ( 16) hydrogen bonds : bond 0.04590 ( 406) hydrogen bonds : angle 6.09230 ( 1122) link_BETA1-4 : bond 0.00045 ( 1) link_BETA1-4 : angle 0.99869 ( 3) link_NAG-ASN : bond 0.00513 ( 4) link_NAG-ASN : angle 3.26410 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 311 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7310 (pp30) cc_final: 0.6791 (pp30) REVERT: A 53 LYS cc_start: 0.7821 (ptpp) cc_final: 0.7557 (ptpt) REVERT: A 234 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7461 (ptmt) REVERT: A 328 MET cc_start: 0.6250 (tpp) cc_final: 0.5789 (tpp) REVERT: A 346 GLU cc_start: 0.6768 (tm-30) cc_final: 0.6411 (tm-30) REVERT: A 404 LYS cc_start: 0.7698 (mttp) cc_final: 0.7370 (mtmt) REVERT: A 523 LYS cc_start: 0.7599 (ttpt) cc_final: 0.7170 (ttpp) REVERT: A 558 LEU cc_start: 0.8740 (tp) cc_final: 0.8435 (tp) REVERT: A 570 LYS cc_start: 0.7227 (tmmt) cc_final: 0.6951 (tmmt) REVERT: A 583 ASN cc_start: 0.7675 (p0) cc_final: 0.7423 (p0) REVERT: A 632 ASP cc_start: 0.7814 (t0) cc_final: 0.7556 (t0) REVERT: A 660 TRP cc_start: 0.7582 (p-90) cc_final: 0.6137 (p90) REVERT: B 817 LYS cc_start: 0.7708 (mmtt) cc_final: 0.7454 (mmtt) REVERT: B 841 MET cc_start: 0.4006 (pmm) cc_final: 0.3658 (pmm) REVERT: B 857 ASN cc_start: 0.7582 (t0) cc_final: 0.7204 (t0) REVERT: B 934 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6992 (mm-30) REVERT: B 1169 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7824 (mm-30) REVERT: B 1288 TRP cc_start: 0.7631 (t60) cc_final: 0.7212 (t-100) REVERT: B 1369 LYS cc_start: 0.8591 (mtpt) cc_final: 0.8300 (mtpp) REVERT: B 1389 MET cc_start: 0.5954 (pmm) cc_final: 0.5680 (pmm) REVERT: C 1465 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7349 (ttm-80) REVERT: C 1510 ARG cc_start: 0.6691 (ptm-80) cc_final: 0.6452 (ptm-80) REVERT: D 53 MET cc_start: 0.5090 (mtm) cc_final: 0.4845 (mtm) REVERT: D 55 GLU cc_start: 0.4722 (pp20) cc_final: 0.3969 (pp20) outliers start: 22 outliers final: 16 residues processed: 322 average time/residue: 0.2476 time to fit residues: 110.0278 Evaluate side-chains 336 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 317 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 1149 LEU Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1301 SER Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1406 HIS Chi-restraints excluded: chain C residue 1465 ARG Chi-restraints excluded: chain C residue 1466 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.0970 chunk 88 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN B1385 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.130121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.109865 restraints weight = 56120.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.115231 restraints weight = 21619.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.118514 restraints weight = 10972.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.120582 restraints weight = 6748.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.121892 restraints weight = 4808.812| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11871 Z= 0.215 Angle : 0.602 8.438 16128 Z= 0.314 Chirality : 0.044 0.262 1835 Planarity : 0.005 0.055 2077 Dihedral : 5.003 48.153 1715 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.07 % Allowed : 14.06 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -1.30 (0.21), residues: 1473 helix: 0.28 (0.32), residues: 266 sheet: -0.97 (0.23), residues: 503 loop : -1.13 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 337 TYR 0.016 0.002 TYR A 548 PHE 0.020 0.002 PHE A 74 TRP 0.011 0.002 TRP B1316 HIS 0.006 0.001 HIS A 552 Details of bonding type rmsd covalent geometry : bond 0.00464 (11858) covalent geometry : angle 0.59271 (16097) SS BOND : bond 0.00428 ( 8) SS BOND : angle 1.86273 ( 16) hydrogen bonds : bond 0.04552 ( 406) hydrogen bonds : angle 5.99975 ( 1122) link_BETA1-4 : bond 0.00336 ( 1) link_BETA1-4 : angle 1.58963 ( 3) link_NAG-ASN : bond 0.00627 ( 4) link_NAG-ASN : angle 3.32946 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 331 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7359 (pp30) cc_final: 0.6840 (pp30) REVERT: A 53 LYS cc_start: 0.7911 (ptpp) cc_final: 0.7620 (ptpt) REVERT: A 231 PHE cc_start: 0.8418 (p90) cc_final: 0.8137 (p90) REVERT: A 234 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7514 (ptmt) REVERT: A 328 MET cc_start: 0.6260 (tpp) cc_final: 0.5910 (tpp) REVERT: A 346 GLU cc_start: 0.6771 (tm-30) cc_final: 0.6435 (tm-30) REVERT: A 404 LYS cc_start: 0.7825 (mttp) cc_final: 0.7510 (mtmt) REVERT: A 523 LYS cc_start: 0.7686 (ttpt) cc_final: 0.7255 (ttpp) REVERT: A 558 LEU cc_start: 0.8699 (tp) cc_final: 0.8366 (tp) REVERT: A 570 LYS cc_start: 0.7274 (tmmt) cc_final: 0.7024 (tmmt) REVERT: A 632 ASP cc_start: 0.7802 (t0) cc_final: 0.7548 (t0) REVERT: A 660 TRP cc_start: 0.7703 (p-90) cc_final: 0.6198 (p90) REVERT: B 817 LYS cc_start: 0.7792 (mmtt) cc_final: 0.7570 (mmtt) REVERT: B 841 MET cc_start: 0.4057 (pmm) cc_final: 0.3768 (pmm) REVERT: B 847 GLU cc_start: 0.6612 (tp30) cc_final: 0.6406 (tp30) REVERT: B 857 ASN cc_start: 0.7676 (t0) cc_final: 0.7227 (t0) REVERT: B 934 GLU cc_start: 0.7308 (mm-30) cc_final: 0.7012 (mm-30) REVERT: B 1169 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7745 (mm-30) REVERT: B 1288 TRP cc_start: 0.7669 (t60) cc_final: 0.7432 (t-100) REVERT: B 1317 ILE cc_start: 0.8330 (pt) cc_final: 0.7929 (mt) REVERT: B 1369 LYS cc_start: 0.8577 (mtpt) cc_final: 0.8279 (mtpp) REVERT: B 1389 MET cc_start: 0.6016 (pmm) cc_final: 0.5739 (pmm) REVERT: D 6 GLU cc_start: 0.6863 (tp30) cc_final: 0.6542 (tp30) REVERT: D 53 MET cc_start: 0.5090 (mtm) cc_final: 0.4841 (mtm) outliers start: 26 outliers final: 23 residues processed: 342 average time/residue: 0.2517 time to fit residues: 119.7463 Evaluate side-chains 342 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 317 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1149 LEU Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1301 SER Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1406 HIS Chi-restraints excluded: chain C residue 1466 VAL Chi-restraints excluded: chain C residue 1536 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 8 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 54 optimal weight: 0.1980 chunk 73 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.131160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.110808 restraints weight = 56035.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.116243 restraints weight = 21507.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.119572 restraints weight = 10883.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.121663 restraints weight = 6711.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.122992 restraints weight = 4756.103| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11871 Z= 0.149 Angle : 0.575 8.551 16128 Z= 0.297 Chirality : 0.043 0.232 1835 Planarity : 0.004 0.049 2077 Dihedral : 4.892 46.540 1715 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.30 % Allowed : 15.33 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -1.15 (0.22), residues: 1473 helix: 0.42 (0.32), residues: 266 sheet: -0.87 (0.23), residues: 505 loop : -1.05 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 337 TYR 0.015 0.001 TYR B1198 PHE 0.015 0.001 PHE A 74 TRP 0.007 0.001 TRP D 32 HIS 0.008 0.001 HIS C1495 Details of bonding type rmsd covalent geometry : bond 0.00332 (11858) covalent geometry : angle 0.56633 (16097) SS BOND : bond 0.00308 ( 8) SS BOND : angle 1.67815 ( 16) hydrogen bonds : bond 0.04145 ( 406) hydrogen bonds : angle 5.78550 ( 1122) link_BETA1-4 : bond 0.00004 ( 1) link_BETA1-4 : angle 1.12531 ( 3) link_NAG-ASN : bond 0.00391 ( 4) link_NAG-ASN : angle 3.10357 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 316 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7297 (pp30) cc_final: 0.6774 (pp30) REVERT: A 53 LYS cc_start: 0.7889 (ptpp) cc_final: 0.7599 (ptpt) REVERT: A 150 TYR cc_start: 0.7667 (m-80) cc_final: 0.7454 (m-80) REVERT: A 231 PHE cc_start: 0.8307 (p90) cc_final: 0.8065 (p90) REVERT: A 234 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7530 (ptmt) REVERT: A 302 GLN cc_start: 0.8371 (pm20) cc_final: 0.8126 (pm20) REVERT: A 328 MET cc_start: 0.6253 (tpp) cc_final: 0.5926 (tpp) REVERT: A 346 GLU cc_start: 0.6782 (tm-30) cc_final: 0.6423 (tm-30) REVERT: A 404 LYS cc_start: 0.7815 (mttp) cc_final: 0.7505 (mtmt) REVERT: A 523 LYS cc_start: 0.7672 (ttpt) cc_final: 0.7238 (ttpp) REVERT: A 558 LEU cc_start: 0.8678 (tp) cc_final: 0.8386 (tp) REVERT: A 570 LYS cc_start: 0.7246 (tmmt) cc_final: 0.7006 (tmmt) REVERT: A 632 ASP cc_start: 0.7815 (t0) cc_final: 0.7554 (t0) REVERT: A 660 TRP cc_start: 0.7698 (p-90) cc_final: 0.6162 (p90) REVERT: B 817 LYS cc_start: 0.7762 (mmtt) cc_final: 0.7541 (mmtt) REVERT: B 841 MET cc_start: 0.4014 (pmm) cc_final: 0.3724 (pmm) REVERT: B 847 GLU cc_start: 0.6637 (tp30) cc_final: 0.6412 (tp30) REVERT: B 857 ASN cc_start: 0.7633 (t0) cc_final: 0.7231 (t0) REVERT: B 934 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6984 (mm-30) REVERT: B 1169 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7693 (mm-30) REVERT: B 1288 TRP cc_start: 0.7605 (t60) cc_final: 0.7362 (t-100) REVERT: B 1369 LYS cc_start: 0.8561 (mtpt) cc_final: 0.8262 (mtpp) REVERT: B 1389 MET cc_start: 0.5990 (pmm) cc_final: 0.5694 (pmm) REVERT: D 6 GLU cc_start: 0.6928 (tp30) cc_final: 0.6648 (tp30) REVERT: D 53 MET cc_start: 0.5099 (mtm) cc_final: 0.4839 (mtm) outliers start: 29 outliers final: 20 residues processed: 330 average time/residue: 0.2524 time to fit residues: 116.0491 Evaluate side-chains 337 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 315 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1301 SER Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1406 HIS Chi-restraints excluded: chain C residue 1536 VAL Chi-restraints excluded: chain D residue 55 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN B1057 GLN B1129 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.126187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.106267 restraints weight = 56326.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.111533 restraints weight = 21833.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.114729 restraints weight = 11122.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.116749 restraints weight = 6865.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.117797 restraints weight = 4893.491| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 11871 Z= 0.345 Angle : 0.690 8.373 16128 Z= 0.366 Chirality : 0.047 0.299 1835 Planarity : 0.006 0.056 2077 Dihedral : 5.355 48.528 1715 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.62 % Allowed : 15.33 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -1.71 (0.21), residues: 1473 helix: -0.06 (0.31), residues: 267 sheet: -1.16 (0.23), residues: 507 loop : -1.46 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 337 TYR 0.021 0.003 TYR A 548 PHE 0.044 0.003 PHE D 33 TRP 0.017 0.003 TRP B 784 HIS 0.009 0.002 HIS C1495 Details of bonding type rmsd covalent geometry : bond 0.00743 (11858) covalent geometry : angle 0.68026 (16097) SS BOND : bond 0.00602 ( 8) SS BOND : angle 2.27067 ( 16) hydrogen bonds : bond 0.04849 ( 406) hydrogen bonds : angle 6.07887 ( 1122) link_BETA1-4 : bond 0.00664 ( 1) link_BETA1-4 : angle 2.57031 ( 3) link_NAG-ASN : bond 0.00918 ( 4) link_NAG-ASN : angle 3.27048 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 333 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7284 (pp30) cc_final: 0.6855 (pp30) REVERT: A 53 LYS cc_start: 0.8117 (ptpp) cc_final: 0.7806 (ptpt) REVERT: A 201 ASP cc_start: 0.7144 (p0) cc_final: 0.6901 (p0) REVERT: A 231 PHE cc_start: 0.8582 (p90) cc_final: 0.8297 (p90) REVERT: A 234 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7496 (ptmt) REVERT: A 318 GLU cc_start: 0.6676 (tm-30) cc_final: 0.6262 (tp30) REVERT: A 346 GLU cc_start: 0.6821 (tm-30) cc_final: 0.6434 (tm-30) REVERT: A 404 LYS cc_start: 0.7875 (mttp) cc_final: 0.7588 (mtmt) REVERT: A 523 LYS cc_start: 0.7805 (ttpt) cc_final: 0.7345 (ttpp) REVERT: A 558 LEU cc_start: 0.8671 (tp) cc_final: 0.8375 (tp) REVERT: A 632 ASP cc_start: 0.7799 (t0) cc_final: 0.7563 (t0) REVERT: A 660 TRP cc_start: 0.7782 (p-90) cc_final: 0.6190 (p90) REVERT: B 801 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.5212 (p0) REVERT: B 841 MET cc_start: 0.4095 (pmm) cc_final: 0.3785 (pmm) REVERT: B 934 GLU cc_start: 0.7258 (mm-30) cc_final: 0.7005 (mm-30) REVERT: B 1015 MET cc_start: 0.7616 (mmm) cc_final: 0.6945 (mmm) REVERT: B 1016 ILE cc_start: 0.7687 (mm) cc_final: 0.7264 (tp) REVERT: B 1166 GLN cc_start: 0.7794 (tp40) cc_final: 0.7039 (tp40) REVERT: B 1169 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7800 (mm-30) REVERT: B 1178 PHE cc_start: 0.7661 (t80) cc_final: 0.7193 (t80) REVERT: B 1263 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6176 (tt0) REVERT: B 1288 TRP cc_start: 0.7746 (t60) cc_final: 0.7493 (t-100) REVERT: B 1369 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8404 (mtpp) REVERT: B 1389 MET cc_start: 0.6165 (pmm) cc_final: 0.5949 (pmm) REVERT: D 6 GLU cc_start: 0.6814 (tp30) cc_final: 0.6503 (tp30) REVERT: D 97 ARG cc_start: 0.7897 (ptp-110) cc_final: 0.7157 (ttm170) outliers start: 33 outliers final: 25 residues processed: 347 average time/residue: 0.2588 time to fit residues: 123.7315 Evaluate side-chains 349 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 320 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 801 ASP Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1263 GLU Chi-restraints excluded: chain B residue 1301 SER Chi-restraints excluded: chain B residue 1329 VAL Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1406 HIS Chi-restraints excluded: chain C residue 1466 VAL Chi-restraints excluded: chain C residue 1536 VAL Chi-restraints excluded: chain C residue 1566 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 64 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN B1092 GLN ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1129 GLN ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1176 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.128836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.108827 restraints weight = 55643.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114204 restraints weight = 21510.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.117437 restraints weight = 10938.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.119446 restraints weight = 6780.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.120669 restraints weight = 4822.648| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11871 Z= 0.171 Angle : 0.607 7.420 16128 Z= 0.314 Chirality : 0.044 0.281 1835 Planarity : 0.005 0.052 2077 Dihedral : 5.083 45.590 1715 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.99 % Allowed : 17.32 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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 (0.21), residues: 1473 helix: 0.29 (0.32), residues: 267 sheet: -1.10 (0.22), residues: 515 loop : -1.30 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1055 TYR 0.014 0.002 TYR B1198 PHE 0.020 0.002 PHE D 33 TRP 0.007 0.001 TRP A 660 HIS 0.008 0.001 HIS C1495 Details of bonding type rmsd covalent geometry : bond 0.00375 (11858) covalent geometry : angle 0.59862 (16097) SS BOND : bond 0.00351 ( 8) SS BOND : angle 1.98799 ( 16) hydrogen bonds : bond 0.04133 ( 406) hydrogen bonds : angle 5.72865 ( 1122) link_BETA1-4 : bond 0.00115 ( 1) link_BETA1-4 : angle 1.17719 ( 3) link_NAG-ASN : bond 0.00435 ( 4) link_NAG-ASN : angle 2.95680 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 327 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7215 (pp30) cc_final: 0.6754 (pp30) REVERT: A 53 LYS cc_start: 0.8070 (ptpp) cc_final: 0.7776 (ptpt) REVERT: A 150 TYR cc_start: 0.7795 (m-80) cc_final: 0.7489 (m-80) REVERT: A 234 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7496 (ptmt) REVERT: A 346 GLU cc_start: 0.6761 (tm-30) cc_final: 0.5744 (tm-30) REVERT: A 351 GLU cc_start: 0.7385 (pm20) cc_final: 0.7125 (mp0) REVERT: A 404 LYS cc_start: 0.7847 (mttp) cc_final: 0.7529 (mtmt) REVERT: A 521 GLU cc_start: 0.7313 (tp30) cc_final: 0.7064 (tp30) REVERT: A 523 LYS cc_start: 0.7791 (ttpt) cc_final: 0.7323 (ttpp) REVERT: A 542 TYR cc_start: 0.7734 (m-80) cc_final: 0.7350 (m-80) REVERT: A 568 GLU cc_start: 0.7078 (pm20) cc_final: 0.6757 (mp0) REVERT: A 570 LYS cc_start: 0.6968 (tmmt) cc_final: 0.6734 (tmmt) REVERT: A 632 ASP cc_start: 0.7791 (t0) cc_final: 0.7516 (t0) REVERT: A 660 TRP cc_start: 0.7782 (p-90) cc_final: 0.6218 (p90) REVERT: B 801 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.5186 (p0) REVERT: B 841 MET cc_start: 0.3958 (pmm) cc_final: 0.3590 (pmm) REVERT: B 857 ASN cc_start: 0.7683 (t0) cc_final: 0.7281 (t0) REVERT: B 934 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6848 (mm-30) REVERT: B 1015 MET cc_start: 0.7563 (mmm) cc_final: 0.7038 (mmm) REVERT: B 1169 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7763 (mm-30) REVERT: B 1178 PHE cc_start: 0.7519 (t80) cc_final: 0.7034 (t80) REVERT: B 1288 TRP cc_start: 0.7638 (t60) cc_final: 0.7302 (t-100) REVERT: B 1369 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8351 (mtpp) REVERT: B 1389 MET cc_start: 0.6127 (pmm) cc_final: 0.5906 (pmm) REVERT: D 6 GLU cc_start: 0.6938 (tp30) cc_final: 0.6713 (tp30) outliers start: 25 outliers final: 20 residues processed: 339 average time/residue: 0.2544 time to fit residues: 118.8601 Evaluate side-chains 348 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 325 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 801 ASP Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1301 SER Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1406 HIS Chi-restraints excluded: chain C residue 1465 ARG Chi-restraints excluded: chain C residue 1536 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 82 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107372 restraints weight = 56287.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112698 restraints weight = 21753.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.115890 restraints weight = 11053.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.117931 restraints weight = 6830.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.119110 restraints weight = 4854.153| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 11871 Z= 0.267 Angle : 0.660 7.914 16128 Z= 0.344 Chirality : 0.046 0.278 1835 Planarity : 0.005 0.051 2077 Dihedral : 5.258 45.536 1715 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.30 % Allowed : 17.39 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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 (0.21), residues: 1473 helix: 0.11 (0.32), residues: 267 sheet: -1.11 (0.23), residues: 497 loop : -1.50 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 337 TYR 0.026 0.002 TYR B1198 PHE 0.024 0.002 PHE A 202 TRP 0.012 0.002 TRP B 784 HIS 0.009 0.002 HIS C1495 Details of bonding type rmsd covalent geometry : bond 0.00582 (11858) covalent geometry : angle 0.64988 (16097) SS BOND : bond 0.00383 ( 8) SS BOND : angle 2.40214 ( 16) hydrogen bonds : bond 0.04437 ( 406) hydrogen bonds : angle 5.84876 ( 1122) link_BETA1-4 : bond 0.00529 ( 1) link_BETA1-4 : angle 1.91301 ( 3) link_NAG-ASN : bond 0.00695 ( 4) link_NAG-ASN : angle 3.14664 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 322 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7205 (pp30) cc_final: 0.6736 (pp30) REVERT: A 53 LYS cc_start: 0.8112 (ptpp) cc_final: 0.7803 (ptpt) REVERT: A 234 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7513 (ptmt) REVERT: A 261 GLU cc_start: 0.6841 (pp20) cc_final: 0.6477 (pp20) REVERT: A 318 GLU cc_start: 0.6638 (tm-30) cc_final: 0.6402 (tp30) REVERT: A 346 GLU cc_start: 0.6776 (tm-30) cc_final: 0.6435 (tm-30) REVERT: A 377 HIS cc_start: 0.8225 (m-70) cc_final: 0.7917 (m90) REVERT: A 404 LYS cc_start: 0.7875 (mttp) cc_final: 0.7597 (mtmt) REVERT: A 523 LYS cc_start: 0.7815 (ttpt) cc_final: 0.7368 (ttpp) REVERT: A 542 TYR cc_start: 0.7797 (m-80) cc_final: 0.7380 (m-80) REVERT: A 632 ASP cc_start: 0.7797 (t0) cc_final: 0.7537 (t0) REVERT: A 660 TRP cc_start: 0.7832 (p-90) cc_final: 0.6256 (p90) REVERT: B 801 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.5137 (p0) REVERT: B 841 MET cc_start: 0.3976 (pmm) cc_final: 0.3586 (pmm) REVERT: B 857 ASN cc_start: 0.7700 (t0) cc_final: 0.7279 (t0) REVERT: B 934 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6812 (mm-30) REVERT: B 1015 MET cc_start: 0.7682 (mmm) cc_final: 0.7089 (mmm) REVERT: B 1166 GLN cc_start: 0.7812 (tp40) cc_final: 0.7082 (tp40) REVERT: B 1169 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7799 (mm-30) REVERT: B 1178 PHE cc_start: 0.7524 (t80) cc_final: 0.7107 (t80) REVERT: B 1288 TRP cc_start: 0.7727 (t60) cc_final: 0.7418 (t-100) REVERT: B 1369 LYS cc_start: 0.8636 (mtpt) cc_final: 0.8372 (mtpp) REVERT: B 1389 MET cc_start: 0.6201 (pmm) cc_final: 0.5993 (pmm) REVERT: D 6 GLU cc_start: 0.6914 (tp30) cc_final: 0.6673 (tp30) outliers start: 29 outliers final: 24 residues processed: 335 average time/residue: 0.2560 time to fit residues: 117.8552 Evaluate side-chains 345 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 318 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 801 ASP Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 1005 ARG Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1301 SER Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1406 HIS Chi-restraints excluded: chain C residue 1465 ARG Chi-restraints excluded: chain C residue 1536 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.126221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.106691 restraints weight = 55427.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.111936 restraints weight = 21323.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.115049 restraints weight = 10787.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.117033 restraints weight = 6635.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.118308 restraints weight = 4697.907| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 11871 Z= 0.323 Angle : 0.712 10.052 16128 Z= 0.375 Chirality : 0.047 0.266 1835 Planarity : 0.006 0.053 2077 Dihedral : 5.583 45.685 1715 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.62 % Allowed : 17.79 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -1.97 (0.21), residues: 1473 helix: -0.19 (0.31), residues: 264 sheet: -1.26 (0.22), residues: 508 loop : -1.71 (0.21), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 337 TYR 0.027 0.003 TYR B1198 PHE 0.031 0.003 PHE A 74 TRP 0.021 0.002 TRP B1077 HIS 0.010 0.002 HIS C1495 Details of bonding type rmsd covalent geometry : bond 0.00693 (11858) covalent geometry : angle 0.70235 (16097) SS BOND : bond 0.00451 ( 8) SS BOND : angle 2.43008 ( 16) hydrogen bonds : bond 0.04708 ( 406) hydrogen bonds : angle 6.00373 ( 1122) link_BETA1-4 : bond 0.00796 ( 1) link_BETA1-4 : angle 2.05401 ( 3) link_NAG-ASN : bond 0.00887 ( 4) link_NAG-ASN : angle 3.29631 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2946 Ramachandran restraints generated. 1473 Oldfield, 0 Emsley, 1473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 326 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLN cc_start: 0.7165 (pp30) cc_final: 0.6713 (pp30) REVERT: A 53 LYS cc_start: 0.8120 (ptpp) cc_final: 0.7827 (ptpt) REVERT: A 135 SER cc_start: 0.8565 (t) cc_final: 0.8008 (p) REVERT: A 191 VAL cc_start: 0.8111 (t) cc_final: 0.7731 (p) REVERT: A 224 GLU cc_start: 0.7424 (pm20) cc_final: 0.7216 (pm20) REVERT: A 234 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7509 (ptmt) REVERT: A 314 LEU cc_start: 0.7998 (mm) cc_final: 0.7542 (mp) REVERT: A 346 GLU cc_start: 0.6879 (tm-30) cc_final: 0.6633 (tm-30) REVERT: A 377 HIS cc_start: 0.8233 (m-70) cc_final: 0.7939 (m90) REVERT: A 378 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7770 (pt) REVERT: A 404 LYS cc_start: 0.7941 (mttp) cc_final: 0.7170 (mtpp) REVERT: A 521 GLU cc_start: 0.7398 (tp30) cc_final: 0.7081 (tp30) REVERT: A 523 LYS cc_start: 0.7869 (ttpt) cc_final: 0.7385 (ttpp) REVERT: A 542 TYR cc_start: 0.7837 (m-80) cc_final: 0.7449 (m-80) REVERT: A 568 GLU cc_start: 0.7342 (pm20) cc_final: 0.6954 (mp0) REVERT: A 632 ASP cc_start: 0.7806 (t0) cc_final: 0.7549 (t0) REVERT: A 660 TRP cc_start: 0.7865 (p-90) cc_final: 0.6293 (p90) REVERT: B 841 MET cc_start: 0.4008 (pmm) cc_final: 0.3520 (pmm) REVERT: B 934 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6789 (mm-30) REVERT: B 942 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6665 (mt-10) REVERT: B 1166 GLN cc_start: 0.7775 (tp40) cc_final: 0.7069 (tp40) REVERT: B 1169 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7743 (mm-30) REVERT: B 1263 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6138 (tt0) REVERT: B 1288 TRP cc_start: 0.7824 (t60) cc_final: 0.7512 (t-100) REVERT: B 1369 LYS cc_start: 0.8653 (mtpt) cc_final: 0.8393 (mtpp) REVERT: C 1518 GLU cc_start: 0.6239 (mp0) cc_final: 0.6010 (mp0) REVERT: D 6 GLU cc_start: 0.6844 (tp30) cc_final: 0.6535 (tp30) REVERT: D 104 VAL cc_start: 0.7279 (m) cc_final: 0.7060 (p) outliers start: 33 outliers final: 29 residues processed: 339 average time/residue: 0.2690 time to fit residues: 123.6574 Evaluate side-chains 355 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 322 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 801 ASP Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 1005 ARG Chi-restraints excluded: chain B residue 1147 ILE Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1263 GLU Chi-restraints excluded: chain B residue 1301 SER Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1399 ILE Chi-restraints excluded: chain B residue 1406 HIS Chi-restraints excluded: chain C residue 1465 ARG Chi-restraints excluded: chain C residue 1490 LEU Chi-restraints excluded: chain C residue 1536 VAL Chi-restraints excluded: chain C residue 1566 CYS Chi-restraints excluded: chain D residue 80 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 33 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 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 = 0.3699 r_free = 0.3699 target = 0.126597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.106935 restraints weight = 55574.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112159 restraints weight = 21660.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.115337 restraints weight = 11056.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.117037 restraints weight = 6831.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.118456 restraints weight = 5045.778| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.283 11871 Z= 0.351 Angle : 0.943 58.886 16128 Z= 0.544 Chirality : 0.049 0.822 1835 Planarity : 0.006 0.053 2077 Dihedral : 5.586 45.675 1715 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.86 % Allowed : 18.27 % Favored : 78.87 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.75 % 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: -1.99 (0.21), residues: 1473 helix: -0.20 (0.31), residues: 264 sheet: -1.28 (0.22), residues: 508 loop : -1.72 (0.21), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 337 TYR 0.023 0.002 TYR B1198 PHE 0.030 0.002 PHE A 74 TRP 0.017 0.002 TRP B1077 HIS 0.008 0.001 HIS C1495 Details of bonding type rmsd covalent geometry : bond 0.00744 (11858) covalent geometry : angle 0.91792 (16097) SS BOND : bond 0.00458 ( 8) SS BOND : angle 2.33319 ( 16) hydrogen bonds : bond 0.04664 ( 406) hydrogen bonds : angle 6.00215 ( 1122) link_BETA1-4 : bond 0.00712 ( 1) link_BETA1-4 : angle 2.65203 ( 3) link_NAG-ASN : bond 0.00875 ( 4) link_NAG-ASN : angle 7.52208 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3937.41 seconds wall clock time: 67 minutes 41.80 seconds (4061.80 seconds total)