Starting phenix.real_space_refine on Thu Mar 5 15:07:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b2p_11989/03_2026/7b2p_11989_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b2p_11989/03_2026/7b2p_11989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7b2p_11989/03_2026/7b2p_11989_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b2p_11989/03_2026/7b2p_11989_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7b2p_11989/03_2026/7b2p_11989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b2p_11989/03_2026/7b2p_11989.map" } resolution = 3.43 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= 0.024 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 42 5.16 5 C 7400 2.51 5 N 2019 2.21 5 O 2229 1.98 5 H 11497 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s 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: 23187 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: 9363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 9363 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 27, 'TRANS': 582} Chain breaks: 3 Chain: "C" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1980 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "D" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1767 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} 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: 3.03, per 1000 atoms: 0.13 Number of scatterers: 23187 At special positions: 0 Unit cell: (141.933, 118.277, 114.163, 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 42 16.00 O 2229 8.00 N 2019 7.00 C 7400 6.00 H 11497 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1583 " - pdb=" SG CYS C1588 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " 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: 1.46 Conformation dependent library (CDL) restraints added in 724.6 milliseconds 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2780 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 28 sheets defined 18.9% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 315 through 326 Processing helix chain 'A' and resid 329 through 333 Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 642 through 650 Processing helix chain 'B' and resid 996 through 1002 removed outlier: 3.533A pdb=" N VAL B1000 " --> pdb=" O SER B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1032 Proline residue: B1020 - end of helix Processing helix chain 'B' and resid 1038 through 1058 removed outlier: 3.993A pdb=" N LYS B1042 " --> pdb=" O PRO B1038 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP B1043 " --> pdb=" O PRO B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1090 Processing helix chain 'B' and resid 1096 through 1110 removed outlier: 4.400A pdb=" N LEU B1100 " --> pdb=" O SER B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1130 removed outlier: 3.706A pdb=" N MET B1128 " --> pdb=" O ASP B1125 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY B1130 " --> pdb=" O SER B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1152 Processing helix chain 'B' and resid 1161 through 1185 removed outlier: 3.550A pdb=" N ALA B1185 " --> pdb=" O GLU B1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 1189 through 1203 Processing helix chain 'B' and resid 1206 through 1221 Processing helix chain 'B' and resid 1258 through 1275 Processing helix chain 'B' and resid 1281 through 1294 Processing helix chain 'B' and resid 1302 through 1320 Processing helix chain 'C' and resid 1498 through 1507 removed outlier: 3.670A pdb=" N GLU C1502 " --> pdb=" O ARG C1498 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS C1503 " --> pdb=" O ALA C1499 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C1504 " --> pdb=" O ASP C1500 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C1505 " --> pdb=" O LEU C1501 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C1507 " --> pdb=" O LYS C1503 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.510A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 87 removed outlier: 7.619A pdb=" N SER A 38 " --> pdb=" O PRO A 28 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 42 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 3.835A pdb=" N ASN A 60 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL A 66 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 145 Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 150 Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 191 removed outlier: 5.903A pdb=" N VAL A 178 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS A 188 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 176 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU A 190 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE A 174 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 241 through 247 removed outlier: 4.052A pdb=" N MET A 262 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 251 through 252 removed outlier: 3.613A pdb=" N ILE A 252 " --> pdb=" O TYR A 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 293 through 295 Processing sheet with id=AA9, first strand: chain 'A' and resid 293 through 295 Processing sheet with id=AB1, first strand: chain 'A' and resid 367 through 370 Processing sheet with id=AB2, first strand: chain 'A' and resid 418 through 423 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 476 removed outlier: 3.703A pdb=" N LEU A 489 " --> pdb=" O VAL A 531 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 515 through 522 removed outlier: 3.734A pdb=" N PHE A 517 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N HIS A 504 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TYR A 548 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA A 545 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N HIS A 552 " --> pdb=" O HIS A 549 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 515 through 522 removed outlier: 3.734A pdb=" N PHE A 517 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N HIS A 504 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TYR A 548 " --> pdb=" O HIS A 504 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 572 through 574 removed outlier: 3.573A pdb=" N GLU A 592 " --> pdb=" O GLU A 572 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 781 through 783 removed outlier: 6.093A pdb=" N ALA A 603 " --> pdb=" O TRP B 782 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 786 through 789 Processing sheet with id=AB9, first strand: chain 'B' and resid 835 through 836 removed outlier: 3.551A pdb=" N LEU B 855 " --> pdb=" O ARG B 895 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 849 through 851 Processing sheet with id=AC2, first strand: chain 'B' and resid 885 through 889 Processing sheet with id=AC3, first strand: chain 'B' and resid 938 through 948 removed outlier: 3.516A pdb=" N VAL B1380 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 978 " --> pdb=" O LEU B1358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 959 through 960 removed outlier: 3.567A pdb=" N SER B1333 " --> pdb=" O LYS B1340 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1397 through 1405 removed outlier: 3.588A pdb=" N GLU C1534 " --> pdb=" O ILE C1472 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1515 through 1518 Processing sheet with id=AC7, first strand: chain 'C' and resid 1581 through 1583 Processing sheet with id=AC8, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.532A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 45 through 51 removed outlier: 5.395A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER D 110 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 45 through 51 removed outlier: 5.395A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 93 " --> pdb=" O GLN D 39 " (cutoff:3.500A) 494 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.60 Time building geometry restraints manager: 2.14 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: 11495 1.03 - 1.23: 31 1.23 - 1.42: 4952 1.42 - 1.62: 6895 1.62 - 1.81: 66 Bond restraints: 23439 Sorted by residual: bond pdb=" C1 NAG B1803 " pdb=" O5 NAG B1803 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.30e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.06e+00 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 2.32e+00 bond pdb=" C GLN D 13 " pdb=" N PRO D 14 " ideal model delta sigma weight residual 1.332 1.349 -0.017 1.30e-02 5.92e+03 1.81e+00 bond pdb=" C1 NAG B1802 " pdb=" O5 NAG B1802 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.43e+00 ... (remaining 23434 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 39743 1.01 - 2.01: 2401 2.01 - 3.02: 123 3.02 - 4.02: 73 4.02 - 5.03: 14 Bond angle restraints: 42354 Sorted by residual: angle pdb=" N ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta sigma weight residual 114.17 109.61 4.56 1.14e+00 7.69e-01 1.60e+01 angle pdb=" N THR A 75 " pdb=" CA THR A 75 " pdb=" C THR A 75 " ideal model delta sigma weight residual 111.17 115.63 -4.46 1.41e+00 5.03e-01 9.99e+00 angle pdb=" CA THR A 75 " pdb=" C THR A 75 " pdb=" N LEU A 76 " ideal model delta sigma weight residual 114.81 118.48 -3.67 1.42e+00 4.96e-01 6.68e+00 angle pdb=" CA TRP D 47 " pdb=" CB TRP D 47 " pdb=" CG TRP D 47 " ideal model delta sigma weight residual 113.60 118.16 -4.56 1.90e+00 2.77e-01 5.77e+00 angle pdb=" C GLY C1476 " pdb=" N LYS C1477 " pdb=" CA LYS C1477 " ideal model delta sigma weight residual 121.54 125.86 -4.32 1.91e+00 2.74e-01 5.12e+00 ... (remaining 42349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.16: 10384 22.16 - 44.32: 595 44.32 - 66.49: 152 66.49 - 88.65: 12 88.65 - 110.81: 3 Dihedral angle restraints: 11146 sinusoidal: 6156 harmonic: 4990 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 42.29 50.71 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" CB CYS B 876 " pdb=" SG CYS B 876 " pdb=" SG CYS C1590 " pdb=" CB CYS C1590 " ideal model delta sinusoidal sigma weight residual -86.00 -130.75 44.75 1 1.00e+01 1.00e-02 2.78e+01 dihedral pdb=" CB CYS A 567 " pdb=" SG CYS A 567 " pdb=" SG CYS B 820 " pdb=" CB CYS B 820 " ideal model delta sinusoidal sigma weight residual 93.00 49.23 43.77 1 1.00e+01 1.00e-02 2.67e+01 ... (remaining 11143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1660 0.073 - 0.146: 186 0.146 - 0.219: 2 0.219 - 0.292: 0 0.292 - 0.365: 1 Chirality restraints: 1849 Sorted by residual: 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 -2.03 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C1 NAG B1801 " pdb=" ND2 ASN B 862 " pdb=" C2 NAG B1801 " pdb=" O5 NAG B1801 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 226 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.77e-01 ... (remaining 1846 not shown) Planarity restraints: 3522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 47 " -0.024 2.00e-02 2.50e+03 1.25e-02 6.20e+00 pdb=" CG TRP D 47 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP D 47 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP D 47 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 47 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 47 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 47 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 47 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 47 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 47 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP D 47 " -0.007 2.00e-02 2.50e+03 pdb=" HE1 TRP D 47 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP D 47 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 47 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 47 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP D 47 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 465 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO A 466 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 466 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 466 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 778 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO B 779 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 779 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 779 " -0.023 5.00e-02 4.00e+02 ... (remaining 3519 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1320 2.19 - 2.79: 47448 2.79 - 3.39: 62521 3.39 - 4.00: 83347 4.00 - 4.60: 127226 Nonbonded interactions: 321862 Sorted by model distance: nonbonded pdb=" O LEU A 58 " pdb=" H CYS A 68 " model vdw 1.583 2.450 nonbonded pdb=" O LYS A 53 " pdb=" HG SER A 114 " model vdw 1.590 2.450 nonbonded pdb=" OE1 GLN B1398 " pdb=" HE1 TRP C1473 " model vdw 1.600 2.450 nonbonded pdb=" OH TYR D 60 " pdb=" H ILE D 70 " model vdw 1.617 2.450 nonbonded pdb=" O THR C1489 " pdb=" HH TYR C1570 " model vdw 1.622 2.450 ... (remaining 321857 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 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: 0.080 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.930 Find NCS groups from input model: 0.090 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11955 Z= 0.154 Angle : 0.540 7.330 16249 Z= 0.286 Chirality : 0.043 0.365 1849 Planarity : 0.003 0.049 2096 Dihedral : 13.608 110.809 4438 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: -0.25 (0.22), residues: 1495 helix: 1.49 (0.34), residues: 257 sheet: -0.28 (0.23), residues: 524 loop : -0.61 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 979 TYR 0.008 0.001 TYR A 272 PHE 0.027 0.001 PHE A 74 TRP 0.041 0.001 TRP D 47 HIS 0.003 0.001 HIS B1150 Details of bonding type rmsd covalent geometry : bond 0.00328 (11942) covalent geometry : angle 0.52875 (16218) SS BOND : bond 0.00157 ( 8) SS BOND : angle 0.72771 ( 16) hydrogen bonds : bond 0.25355 ( 471) hydrogen bonds : angle 9.72970 ( 1347) link_BETA1-4 : bond 0.00994 ( 1) link_BETA1-4 : angle 3.59135 ( 3) link_NAG-ASN : bond 0.01084 ( 4) link_NAG-ASN : angle 3.68145 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 0.600 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 SER cc_start: 0.7254 (m) cc_final: 0.6882 (p) REVERT: A 107 GLU cc_start: 0.7269 (mm-30) cc_final: 0.7065 (mm-30) REVERT: A 352 MET cc_start: 0.6756 (ptp) cc_final: 0.6496 (ptp) REVERT: A 353 GLU cc_start: 0.7044 (mp0) cc_final: 0.6843 (mp0) REVERT: A 404 LYS cc_start: 0.7710 (mmmt) cc_final: 0.7443 (mmmt) REVERT: A 422 GLN cc_start: 0.7701 (tm-30) cc_final: 0.7111 (tm-30) REVERT: A 433 ILE cc_start: 0.8646 (tt) cc_final: 0.8376 (pt) REVERT: A 642 SER cc_start: 0.8318 (m) cc_final: 0.8044 (p) REVERT: B 815 LYS cc_start: 0.7992 (mttp) cc_final: 0.7715 (mttp) REVERT: B 817 LYS cc_start: 0.7982 (mmtt) cc_final: 0.7715 (mmtp) REVERT: B 910 SER cc_start: 0.7449 (t) cc_final: 0.7213 (p) REVERT: B 968 MET cc_start: 0.7845 (tmm) cc_final: 0.7525 (tmm) REVERT: B 969 ILE cc_start: 0.8831 (mt) cc_final: 0.8360 (mt) REVERT: B 974 PHE cc_start: 0.7611 (t80) cc_final: 0.7376 (t80) REVERT: B 1085 VAL cc_start: 0.8700 (t) cc_final: 0.8428 (p) REVERT: B 1229 TYR cc_start: 0.6102 (m-80) cc_final: 0.5712 (m-80) REVERT: B 1288 TRP cc_start: 0.8076 (t60) cc_final: 0.7856 (t60) REVERT: B 1306 VAL cc_start: 0.7821 (p) cc_final: 0.6868 (p) REVERT: B 1310 ASP cc_start: 0.7123 (m-30) cc_final: 0.6692 (m-30) REVERT: C 1483 MET cc_start: 0.6924 (ptp) cc_final: 0.6237 (ptp) REVERT: C 1527 ASP cc_start: 0.7438 (p0) cc_final: 0.6940 (p0) REVERT: D 78 THR cc_start: 0.8236 (m) cc_final: 0.7918 (p) REVERT: D 102 PHE cc_start: 0.8340 (t80) cc_final: 0.8132 (t80) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.2722 time to fit residues: 157.4410 Evaluate side-chains 367 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.0030 chunk 149 optimal weight: 0.9980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 ASN A 423 GLN B 793 GLN B 949 ASN B1227 ASN B1256 GLN D 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.126257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.110438 restraints weight = 54880.912| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.86 r_work: 0.3349 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11955 Z= 0.159 Angle : 0.621 7.670 16249 Z= 0.322 Chirality : 0.045 0.263 1849 Planarity : 0.004 0.039 2096 Dihedral : 7.125 97.975 1729 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.65 % Allowed : 10.38 % Favored : 87.97 % 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: -0.37 (0.21), residues: 1495 helix: 1.24 (0.32), residues: 265 sheet: -0.33 (0.22), residues: 532 loop : -0.66 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 137 TYR 0.013 0.001 TYR D 105 PHE 0.020 0.001 PHE A 74 TRP 0.025 0.001 TRP D 47 HIS 0.004 0.001 HIS B1150 Details of bonding type rmsd covalent geometry : bond 0.00346 (11942) covalent geometry : angle 0.61238 (16218) SS BOND : bond 0.00638 ( 8) SS BOND : angle 1.17139 ( 16) hydrogen bonds : bond 0.05402 ( 471) hydrogen bonds : angle 6.85500 ( 1347) link_BETA1-4 : bond 0.00045 ( 1) link_BETA1-4 : angle 1.32326 ( 3) link_NAG-ASN : bond 0.00720 ( 4) link_NAG-ASN : angle 3.56422 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 387 time to evaluate : 0.601 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: A 38 SER cc_start: 0.8537 (m) cc_final: 0.8109 (p) REVERT: A 42 GLN cc_start: 0.8052 (pp30) cc_final: 0.7433 (pp30) REVERT: A 62 SER cc_start: 0.7677 (m) cc_final: 0.7242 (p) REVERT: A 121 LEU cc_start: 0.8502 (mt) cc_final: 0.8215 (mp) REVERT: A 289 GLU cc_start: 0.7975 (mp0) cc_final: 0.7761 (mp0) REVERT: A 304 LYS cc_start: 0.8781 (ttpp) cc_final: 0.8451 (ttmm) REVERT: A 352 MET cc_start: 0.8177 (ptp) cc_final: 0.7653 (ptp) REVERT: A 353 GLU cc_start: 0.7717 (mp0) cc_final: 0.7459 (mp0) REVERT: A 404 LYS cc_start: 0.7940 (mmmt) cc_final: 0.7563 (mttm) REVERT: A 433 ILE cc_start: 0.8741 (tt) cc_final: 0.8388 (pt) REVERT: A 642 SER cc_start: 0.8046 (m) cc_final: 0.7656 (p) REVERT: B 801 ASP cc_start: 0.7684 (m-30) cc_final: 0.7475 (m-30) REVERT: B 815 LYS cc_start: 0.8448 (mttp) cc_final: 0.8153 (mttp) REVERT: B 942 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7059 (mm-30) REVERT: B 968 MET cc_start: 0.8223 (tmm) cc_final: 0.7766 (tmm) REVERT: B 969 ILE cc_start: 0.8855 (mt) cc_final: 0.8485 (mt) REVERT: B 974 PHE cc_start: 0.8055 (t80) cc_final: 0.7757 (t80) REVERT: B 1085 VAL cc_start: 0.8619 (t) cc_final: 0.8290 (m) REVERT: B 1129 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8203 (tp40) REVERT: B 1229 TYR cc_start: 0.6752 (m-80) cc_final: 0.6313 (m-80) REVERT: B 1288 TRP cc_start: 0.8321 (t60) cc_final: 0.7947 (t60) REVERT: B 1369 LYS cc_start: 0.7779 (mtpp) cc_final: 0.7445 (mtpp) REVERT: B 1384 TYR cc_start: 0.8182 (p90) cc_final: 0.7612 (p90) REVERT: C 1483 MET cc_start: 0.7502 (ptp) cc_final: 0.6685 (ptp) REVERT: C 1515 PHE cc_start: 0.7917 (p90) cc_final: 0.7715 (p90) REVERT: C 1523 LEU cc_start: 0.8402 (mt) cc_final: 0.8048 (mp) REVERT: C 1527 ASP cc_start: 0.7730 (p0) cc_final: 0.7315 (p0) REVERT: D 46 GLU cc_start: 0.7379 (pm20) cc_final: 0.7153 (pm20) REVERT: D 78 THR cc_start: 0.8174 (m) cc_final: 0.7737 (p) outliers start: 21 outliers final: 12 residues processed: 392 average time/residue: 0.2701 time to fit residues: 145.1595 Evaluate side-chains 387 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 375 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1329 VAL Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain C residue 1505 THR Chi-restraints excluded: chain C residue 1565 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 61 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 146 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1256 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.124426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.108489 restraints weight = 55091.363| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.93 r_work: 0.3346 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11955 Z= 0.162 Angle : 0.578 7.396 16249 Z= 0.297 Chirality : 0.044 0.263 1849 Planarity : 0.004 0.043 2096 Dihedral : 6.937 95.787 1729 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.97 % Allowed : 13.13 % Favored : 84.91 % 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: -0.34 (0.21), residues: 1495 helix: 1.23 (0.32), residues: 267 sheet: -0.20 (0.23), residues: 504 loop : -0.72 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 137 TYR 0.016 0.001 TYR D 105 PHE 0.016 0.001 PHE A 74 TRP 0.025 0.002 TRP D 47 HIS 0.006 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00352 (11942) covalent geometry : angle 0.56942 (16218) SS BOND : bond 0.00522 ( 8) SS BOND : angle 1.34907 ( 16) hydrogen bonds : bond 0.04525 ( 471) hydrogen bonds : angle 6.19040 ( 1347) link_BETA1-4 : bond 0.00184 ( 1) link_BETA1-4 : angle 1.36393 ( 3) link_NAG-ASN : bond 0.00717 ( 4) link_NAG-ASN : angle 3.47051 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 381 time to evaluate : 0.518 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: symmetry clash REVERT: A 38 SER cc_start: 0.8464 (m) cc_final: 0.7977 (p) REVERT: A 62 SER cc_start: 0.7619 (m) cc_final: 0.7129 (p) REVERT: A 116 TRP cc_start: 0.8123 (t60) cc_final: 0.7754 (t60) REVERT: A 244 LYS cc_start: 0.8153 (ptpt) cc_final: 0.7927 (ptpp) REVERT: A 300 GLU cc_start: 0.7595 (mp0) cc_final: 0.7376 (mp0) REVERT: A 304 LYS cc_start: 0.8625 (ttpp) cc_final: 0.8289 (ttpp) REVERT: A 352 MET cc_start: 0.7909 (ptp) cc_final: 0.7665 (ptm) REVERT: A 404 LYS cc_start: 0.7814 (mmmt) cc_final: 0.7468 (mttm) REVERT: A 433 ILE cc_start: 0.8687 (tt) cc_final: 0.8305 (pt) REVERT: A 642 SER cc_start: 0.7937 (m) cc_final: 0.7545 (p) REVERT: B 801 ASP cc_start: 0.7301 (m-30) cc_final: 0.7050 (m-30) REVERT: B 815 LYS cc_start: 0.8434 (mttp) cc_final: 0.8140 (mttp) REVERT: B 817 LYS cc_start: 0.7907 (mmtt) cc_final: 0.7423 (mmtm) REVERT: B 889 VAL cc_start: 0.8577 (p) cc_final: 0.8369 (t) REVERT: B 941 ARG cc_start: 0.7715 (ptp-110) cc_final: 0.7427 (ptp90) REVERT: B 942 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7244 (mm-30) REVERT: B 968 MET cc_start: 0.8058 (tmm) cc_final: 0.7578 (tmm) REVERT: B 969 ILE cc_start: 0.8815 (mt) cc_final: 0.8434 (mt) REVERT: B 974 PHE cc_start: 0.7944 (t80) cc_final: 0.7650 (t80) REVERT: B 1085 VAL cc_start: 0.8519 (t) cc_final: 0.8150 (m) REVERT: B 1129 GLN cc_start: 0.8394 (mm-40) cc_final: 0.7786 (tp40) REVERT: B 1288 TRP cc_start: 0.8188 (t60) cc_final: 0.7751 (t60) REVERT: B 1384 TYR cc_start: 0.8136 (p90) cc_final: 0.7834 (p90) REVERT: C 1483 MET cc_start: 0.7389 (ptp) cc_final: 0.6618 (ptp) REVERT: C 1523 LEU cc_start: 0.8257 (mt) cc_final: 0.7890 (mp) REVERT: C 1527 ASP cc_start: 0.7570 (p0) cc_final: 0.7168 (p0) REVERT: D 76 LYS cc_start: 0.8491 (mmmt) cc_final: 0.8269 (mmmt) REVERT: D 78 THR cc_start: 0.8212 (m) cc_final: 0.7614 (p) REVERT: D 83 MET cc_start: 0.7720 (mpp) cc_final: 0.7454 (mpp) outliers start: 25 outliers final: 20 residues processed: 389 average time/residue: 0.2784 time to fit residues: 147.5712 Evaluate side-chains 386 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 366 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1195 ILE Chi-restraints excluded: chain B residue 1310 ASP Chi-restraints excluded: chain B residue 1329 VAL Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain C residue 1505 THR Chi-restraints excluded: chain C residue 1565 ARG Chi-restraints excluded: chain D residue 22 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 0.0070 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1256 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.124206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.108644 restraints weight = 54409.256| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.78 r_work: 0.3335 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11955 Z= 0.190 Angle : 0.578 7.338 16249 Z= 0.296 Chirality : 0.043 0.268 1849 Planarity : 0.004 0.058 2096 Dihedral : 6.822 92.828 1729 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.04 % Allowed : 14.23 % Favored : 83.73 % 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: -0.39 (0.21), residues: 1495 helix: 1.25 (0.32), residues: 266 sheet: -0.24 (0.22), residues: 534 loop : -0.78 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 137 TYR 0.018 0.002 TYR D 105 PHE 0.018 0.001 PHE A 82 TRP 0.029 0.002 TRP D 47 HIS 0.006 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00409 (11942) covalent geometry : angle 0.56828 (16218) SS BOND : bond 0.00483 ( 8) SS BOND : angle 1.29854 ( 16) hydrogen bonds : bond 0.04054 ( 471) hydrogen bonds : angle 5.78068 ( 1347) link_BETA1-4 : bond 0.00104 ( 1) link_BETA1-4 : angle 1.46416 ( 3) link_NAG-ASN : bond 0.00744 ( 4) link_NAG-ASN : angle 3.60180 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 391 time to evaluate : 0.462 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: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8620 (m) cc_final: 0.8248 (p) REVERT: A 62 SER cc_start: 0.7785 (m) cc_final: 0.7284 (p) REVERT: A 116 TRP cc_start: 0.8161 (t60) cc_final: 0.7745 (t60) REVERT: A 244 LYS cc_start: 0.8364 (ptpt) cc_final: 0.8145 (ptpp) REVERT: A 282 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8501 (m) REVERT: A 300 GLU cc_start: 0.8008 (mp0) cc_final: 0.7730 (mp0) REVERT: A 304 LYS cc_start: 0.8734 (ttpp) cc_final: 0.8429 (ttpp) REVERT: A 352 MET cc_start: 0.8114 (ptp) cc_final: 0.7897 (ptm) REVERT: A 404 LYS cc_start: 0.8008 (mmmt) cc_final: 0.7649 (mttm) REVERT: A 421 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8569 (mm) REVERT: A 433 ILE cc_start: 0.8770 (tt) cc_final: 0.8405 (pt) REVERT: A 585 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7362 (mm-30) REVERT: A 629 ASN cc_start: 0.8197 (t0) cc_final: 0.7990 (t0) REVERT: A 642 SER cc_start: 0.8113 (m) cc_final: 0.7754 (p) REVERT: A 667 LEU cc_start: 0.8209 (mp) cc_final: 0.7967 (tp) REVERT: B 801 ASP cc_start: 0.7635 (m-30) cc_final: 0.7412 (m-30) REVERT: B 815 LYS cc_start: 0.8476 (mttp) cc_final: 0.8191 (mttp) REVERT: B 889 VAL cc_start: 0.8690 (p) cc_final: 0.8456 (t) REVERT: B 941 ARG cc_start: 0.7835 (ptp-110) cc_final: 0.7547 (ptp90) REVERT: B 942 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7485 (mm-30) REVERT: B 968 MET cc_start: 0.8219 (tmm) cc_final: 0.7684 (tmm) REVERT: B 969 ILE cc_start: 0.8924 (mt) cc_final: 0.8557 (mt) REVERT: B 974 PHE cc_start: 0.7954 (t80) cc_final: 0.7512 (t80) REVERT: B 1085 VAL cc_start: 0.8671 (t) cc_final: 0.8325 (m) REVERT: B 1129 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8221 (tp40) REVERT: B 1174 LYS cc_start: 0.8680 (tttt) cc_final: 0.8297 (tttm) REVERT: B 1288 TRP cc_start: 0.8311 (t60) cc_final: 0.7888 (t60) REVERT: B 1355 GLU cc_start: 0.7580 (mp0) cc_final: 0.7222 (mp0) REVERT: B 1384 TYR cc_start: 0.8285 (p90) cc_final: 0.7971 (p90) REVERT: C 1483 MET cc_start: 0.7789 (ptp) cc_final: 0.7095 (ptp) REVERT: C 1487 ASP cc_start: 0.7926 (t0) cc_final: 0.7724 (t0) REVERT: C 1523 LEU cc_start: 0.8422 (mt) cc_final: 0.8131 (mp) REVERT: C 1527 ASP cc_start: 0.7771 (p0) cc_final: 0.7454 (p0) REVERT: D 76 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8289 (mmmt) REVERT: D 78 THR cc_start: 0.8148 (m) cc_final: 0.7505 (p) outliers start: 26 outliers final: 18 residues processed: 399 average time/residue: 0.2689 time to fit residues: 146.1663 Evaluate side-chains 405 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 385 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 1016 ILE Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1165 LYS Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain B residue 1402 THR Chi-restraints excluded: chain C residue 1505 THR Chi-restraints excluded: chain C residue 1565 ARG Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 56 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 144 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.124310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.108866 restraints weight = 53714.595| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.79 r_work: 0.3337 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11955 Z= 0.217 Angle : 0.587 7.413 16249 Z= 0.300 Chirality : 0.043 0.276 1849 Planarity : 0.004 0.053 2096 Dihedral : 6.766 92.159 1729 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.36 % Allowed : 15.25 % Favored : 82.39 % 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: -0.42 (0.21), residues: 1495 helix: 1.25 (0.33), residues: 266 sheet: -0.28 (0.22), residues: 540 loop : -0.80 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 137 TYR 0.019 0.002 TYR D 105 PHE 0.022 0.002 PHE C1494 TRP 0.029 0.002 TRP D 47 HIS 0.007 0.001 HIS B1150 Details of bonding type rmsd covalent geometry : bond 0.00465 (11942) covalent geometry : angle 0.57691 (16218) SS BOND : bond 0.00516 ( 8) SS BOND : angle 1.29526 ( 16) hydrogen bonds : bond 0.04081 ( 471) hydrogen bonds : angle 5.62584 ( 1347) link_BETA1-4 : bond 0.00130 ( 1) link_BETA1-4 : angle 1.52142 ( 3) link_NAG-ASN : bond 0.00696 ( 4) link_NAG-ASN : angle 3.72282 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 402 time to evaluate : 0.525 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: symmetry clash REVERT: A 38 SER cc_start: 0.8636 (m) cc_final: 0.8240 (p) REVERT: A 42 GLN cc_start: 0.7851 (pp30) cc_final: 0.7375 (pp30) REVERT: A 62 SER cc_start: 0.7863 (m) cc_final: 0.7343 (p) REVERT: A 116 TRP cc_start: 0.8116 (t60) cc_final: 0.7669 (t60) REVERT: A 168 ARG cc_start: 0.8504 (mmt-90) cc_final: 0.8267 (mpt180) REVERT: A 244 LYS cc_start: 0.8368 (ptpt) cc_final: 0.8144 (ptpp) REVERT: A 282 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8485 (m) REVERT: A 300 GLU cc_start: 0.7997 (mp0) cc_final: 0.7783 (mp0) REVERT: A 304 LYS cc_start: 0.8738 (ttpp) cc_final: 0.8421 (ttpp) REVERT: A 404 LYS cc_start: 0.8053 (mmmt) cc_final: 0.7722 (mttm) REVERT: A 433 ILE cc_start: 0.8744 (tt) cc_final: 0.8368 (pt) REVERT: A 585 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7426 (mm-30) REVERT: A 629 ASN cc_start: 0.8205 (t0) cc_final: 0.7935 (t0) REVERT: A 642 SER cc_start: 0.8070 (m) cc_final: 0.7715 (p) REVERT: A 667 LEU cc_start: 0.8240 (mp) cc_final: 0.8001 (tp) REVERT: B 785 ARG cc_start: 0.8294 (ptm160) cc_final: 0.7934 (ptm160) REVERT: B 801 ASP cc_start: 0.7659 (m-30) cc_final: 0.7430 (m-30) REVERT: B 815 LYS cc_start: 0.8518 (mttp) cc_final: 0.8205 (mttp) REVERT: B 817 LYS cc_start: 0.7953 (mmtm) cc_final: 0.7705 (mmtm) REVERT: B 889 VAL cc_start: 0.8679 (p) cc_final: 0.8454 (t) REVERT: B 923 VAL cc_start: 0.7839 (t) cc_final: 0.7629 (t) REVERT: B 941 ARG cc_start: 0.7846 (ptp-110) cc_final: 0.7586 (ptp90) REVERT: B 942 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7400 (mm-30) REVERT: B 968 MET cc_start: 0.8133 (tmm) cc_final: 0.7611 (tmm) REVERT: B 969 ILE cc_start: 0.8935 (mt) cc_final: 0.8568 (mt) REVERT: B 974 PHE cc_start: 0.7982 (t80) cc_final: 0.7678 (t80) REVERT: B 1085 VAL cc_start: 0.8649 (t) cc_final: 0.8288 (m) REVERT: B 1129 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8236 (tp40) REVERT: B 1288 TRP cc_start: 0.8328 (t60) cc_final: 0.7881 (t60) REVERT: B 1384 TYR cc_start: 0.8273 (p90) cc_final: 0.7965 (p90) REVERT: C 1483 MET cc_start: 0.7831 (ptp) cc_final: 0.7224 (ptp) REVERT: C 1487 ASP cc_start: 0.8060 (t0) cc_final: 0.7809 (t0) REVERT: C 1515 PHE cc_start: 0.8016 (p90) cc_final: 0.7781 (p90) REVERT: C 1523 LEU cc_start: 0.8452 (mt) cc_final: 0.8128 (mp) REVERT: C 1527 ASP cc_start: 0.7782 (p0) cc_final: 0.7482 (p0) REVERT: D 49 SER cc_start: 0.8512 (p) cc_final: 0.8311 (p) REVERT: D 76 LYS cc_start: 0.8530 (mmmt) cc_final: 0.8269 (mmmt) REVERT: D 78 THR cc_start: 0.8044 (m) cc_final: 0.7383 (p) outliers start: 30 outliers final: 25 residues processed: 410 average time/residue: 0.2918 time to fit residues: 161.5570 Evaluate side-chains 409 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 383 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1165 LYS Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain B residue 1402 THR Chi-restraints excluded: chain C residue 1505 THR Chi-restraints excluded: chain C residue 1565 ARG Chi-restraints excluded: chain D residue 22 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 59 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.122915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.107303 restraints weight = 54372.144| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.84 r_work: 0.3299 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11955 Z= 0.240 Angle : 0.596 7.443 16249 Z= 0.306 Chirality : 0.043 0.277 1849 Planarity : 0.004 0.059 2096 Dihedral : 6.745 91.248 1729 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.44 % Allowed : 17.61 % Favored : 79.95 % 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: -0.50 (0.21), residues: 1495 helix: 1.15 (0.33), residues: 266 sheet: -0.25 (0.22), residues: 525 loop : -0.91 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 137 TYR 0.020 0.002 TYR D 105 PHE 0.020 0.002 PHE C1494 TRP 0.029 0.002 TRP D 47 HIS 0.007 0.001 HIS B1150 Details of bonding type rmsd covalent geometry : bond 0.00512 (11942) covalent geometry : angle 0.58588 (16218) SS BOND : bond 0.00700 ( 8) SS BOND : angle 1.37453 ( 16) hydrogen bonds : bond 0.04092 ( 471) hydrogen bonds : angle 5.58938 ( 1347) link_BETA1-4 : bond 0.00114 ( 1) link_BETA1-4 : angle 1.57487 ( 3) link_NAG-ASN : bond 0.00728 ( 4) link_NAG-ASN : angle 3.83638 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 403 time to evaluate : 0.503 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: A 38 SER cc_start: 0.8639 (m) cc_final: 0.8235 (p) REVERT: A 42 GLN cc_start: 0.7767 (pp30) cc_final: 0.7329 (pp30) REVERT: A 62 SER cc_start: 0.7935 (m) cc_final: 0.7416 (p) REVERT: A 116 TRP cc_start: 0.8139 (t60) cc_final: 0.7601 (t60) REVERT: A 126 ASN cc_start: 0.8427 (p0) cc_final: 0.8171 (p0) REVERT: A 244 LYS cc_start: 0.8398 (ptpt) cc_final: 0.8145 (ptpp) REVERT: A 282 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8466 (m) REVERT: A 300 GLU cc_start: 0.8025 (mp0) cc_final: 0.7805 (mp0) REVERT: A 304 LYS cc_start: 0.8737 (ttpp) cc_final: 0.8413 (ttpp) REVERT: A 379 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.7550 (t) REVERT: A 404 LYS cc_start: 0.8035 (mmmt) cc_final: 0.7721 (mttm) REVERT: A 433 ILE cc_start: 0.8744 (tt) cc_final: 0.8383 (pt) REVERT: A 521 GLU cc_start: 0.7414 (mm-30) cc_final: 0.6884 (mm-30) REVERT: A 629 ASN cc_start: 0.8214 (t0) cc_final: 0.7941 (t0) REVERT: A 642 SER cc_start: 0.8088 (m) cc_final: 0.7721 (p) REVERT: A 667 LEU cc_start: 0.8251 (mp) cc_final: 0.8015 (tp) REVERT: B 801 ASP cc_start: 0.7765 (m-30) cc_final: 0.7498 (m-30) REVERT: B 815 LYS cc_start: 0.8544 (mttp) cc_final: 0.8233 (mttp) REVERT: B 889 VAL cc_start: 0.8642 (p) cc_final: 0.8434 (t) REVERT: B 923 VAL cc_start: 0.7851 (t) cc_final: 0.7360 (m) REVERT: B 941 ARG cc_start: 0.7855 (ptp-110) cc_final: 0.7597 (ptp90) REVERT: B 942 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7367 (mm-30) REVERT: B 968 MET cc_start: 0.8130 (tmm) cc_final: 0.7617 (tmm) REVERT: B 969 ILE cc_start: 0.8937 (mt) cc_final: 0.8582 (mt) REVERT: B 974 PHE cc_start: 0.7983 (t80) cc_final: 0.7682 (t80) REVERT: B 1085 VAL cc_start: 0.8691 (t) cc_final: 0.8320 (m) REVERT: B 1167 ARG cc_start: 0.8320 (mtm180) cc_final: 0.8101 (ttp80) REVERT: B 1288 TRP cc_start: 0.8347 (t60) cc_final: 0.7909 (t60) REVERT: B 1355 GLU cc_start: 0.7547 (mp0) cc_final: 0.7289 (mp0) REVERT: B 1384 TYR cc_start: 0.8284 (p90) cc_final: 0.8009 (p90) REVERT: C 1483 MET cc_start: 0.7903 (ptp) cc_final: 0.7316 (ptp) REVERT: C 1487 ASP cc_start: 0.8063 (t0) cc_final: 0.7740 (t0) REVERT: C 1515 PHE cc_start: 0.8042 (p90) cc_final: 0.7775 (p90) REVERT: C 1523 LEU cc_start: 0.8493 (mt) cc_final: 0.8126 (mp) REVERT: C 1524 LEU cc_start: 0.8557 (mp) cc_final: 0.8310 (mt) REVERT: C 1527 ASP cc_start: 0.7811 (p0) cc_final: 0.7515 (p0) REVERT: D 49 SER cc_start: 0.8530 (p) cc_final: 0.8321 (p) REVERT: D 76 LYS cc_start: 0.8507 (mmmt) cc_final: 0.8262 (mmmt) REVERT: D 78 THR cc_start: 0.8010 (m) cc_final: 0.7344 (p) outliers start: 31 outliers final: 26 residues processed: 412 average time/residue: 0.2989 time to fit residues: 168.2240 Evaluate side-chains 427 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 399 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1165 LYS Chi-restraints excluded: chain B residue 1215 ASN Chi-restraints excluded: chain B residue 1331 LEU Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain B residue 1402 THR Chi-restraints excluded: chain C residue 1505 THR Chi-restraints excluded: chain C residue 1565 ARG Chi-restraints excluded: chain D residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 58 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 25 optimal weight: 0.0980 chunk 79 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.124512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.109089 restraints weight = 53764.192| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.80 r_work: 0.3271 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11955 Z= 0.189 Angle : 0.583 7.329 16249 Z= 0.297 Chirality : 0.043 0.283 1849 Planarity : 0.004 0.060 2096 Dihedral : 6.642 90.883 1729 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.12 % Allowed : 19.42 % Favored : 78.46 % 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: -0.44 (0.22), residues: 1495 helix: 1.31 (0.33), residues: 266 sheet: -0.28 (0.22), residues: 534 loop : -0.86 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 137 TYR 0.018 0.001 TYR D 105 PHE 0.018 0.001 PHE C1494 TRP 0.024 0.002 TRP D 47 HIS 0.006 0.001 HIS B1150 Details of bonding type rmsd covalent geometry : bond 0.00410 (11942) covalent geometry : angle 0.57290 (16218) SS BOND : bond 0.00619 ( 8) SS BOND : angle 1.46418 ( 16) hydrogen bonds : bond 0.03854 ( 471) hydrogen bonds : angle 5.44678 ( 1347) link_BETA1-4 : bond 0.00127 ( 1) link_BETA1-4 : angle 1.46859 ( 3) link_NAG-ASN : bond 0.00740 ( 4) link_NAG-ASN : angle 3.74773 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 405 time to evaluate : 0.596 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: A 38 SER cc_start: 0.8599 (m) cc_final: 0.8200 (p) REVERT: A 42 GLN cc_start: 0.7708 (pp30) cc_final: 0.7305 (pp30) REVERT: A 62 SER cc_start: 0.7920 (m) cc_final: 0.7412 (p) REVERT: A 116 TRP cc_start: 0.8122 (t60) cc_final: 0.7632 (t60) REVERT: A 126 ASN cc_start: 0.8417 (p0) cc_final: 0.8122 (p0) REVERT: A 233 VAL cc_start: 0.8120 (p) cc_final: 0.7884 (t) REVERT: A 244 LYS cc_start: 0.8385 (ptpt) cc_final: 0.8136 (ptpp) REVERT: A 282 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8471 (m) REVERT: A 300 GLU cc_start: 0.8065 (mp0) cc_final: 0.7810 (mp0) REVERT: A 304 LYS cc_start: 0.8723 (ttpp) cc_final: 0.8410 (ttpp) REVERT: A 379 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.7541 (t) REVERT: A 404 LYS cc_start: 0.8007 (mmmt) cc_final: 0.7706 (mttm) REVERT: A 433 ILE cc_start: 0.8730 (tt) cc_final: 0.8374 (pt) REVERT: A 521 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6876 (mm-30) REVERT: A 629 ASN cc_start: 0.8235 (t0) cc_final: 0.8008 (t0) REVERT: A 642 SER cc_start: 0.8116 (m) cc_final: 0.7765 (p) REVERT: A 667 LEU cc_start: 0.8247 (mp) cc_final: 0.8009 (tp) REVERT: B 801 ASP cc_start: 0.7746 (m-30) cc_final: 0.7490 (m-30) REVERT: B 815 LYS cc_start: 0.8575 (mttp) cc_final: 0.8278 (mttp) REVERT: B 889 VAL cc_start: 0.8615 (p) cc_final: 0.8384 (t) REVERT: B 923 VAL cc_start: 0.7832 (t) cc_final: 0.7349 (m) REVERT: B 941 ARG cc_start: 0.7841 (ptp-110) cc_final: 0.7570 (ptp90) REVERT: B 968 MET cc_start: 0.8135 (tmm) cc_final: 0.7614 (tmm) REVERT: B 969 ILE cc_start: 0.8910 (mt) cc_final: 0.8570 (mt) REVERT: B 974 PHE cc_start: 0.7942 (t80) cc_final: 0.7626 (t80) REVERT: B 1085 VAL cc_start: 0.8665 (t) cc_final: 0.8301 (m) REVERT: B 1129 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8252 (tp40) REVERT: B 1167 ARG cc_start: 0.8311 (mtm180) cc_final: 0.8078 (ttp80) REVERT: B 1174 LYS cc_start: 0.8656 (tttt) cc_final: 0.8304 (tttm) REVERT: B 1288 TRP cc_start: 0.8305 (t60) cc_final: 0.7906 (t60) REVERT: B 1355 GLU cc_start: 0.7524 (mp0) cc_final: 0.7246 (mp0) REVERT: B 1358 LEU cc_start: 0.8472 (tt) cc_final: 0.8252 (tt) REVERT: B 1384 TYR cc_start: 0.8311 (p90) cc_final: 0.8040 (p90) REVERT: C 1483 MET cc_start: 0.7863 (ptp) cc_final: 0.7318 (ptp) REVERT: C 1487 ASP cc_start: 0.8031 (t0) cc_final: 0.7706 (t0) REVERT: C 1515 PHE cc_start: 0.8015 (p90) cc_final: 0.7760 (p90) REVERT: C 1523 LEU cc_start: 0.8482 (mt) cc_final: 0.8168 (mp) REVERT: C 1527 ASP cc_start: 0.7826 (p0) cc_final: 0.7541 (p0) REVERT: D 49 SER cc_start: 0.8509 (p) cc_final: 0.8280 (p) REVERT: D 76 LYS cc_start: 0.8499 (mmmt) cc_final: 0.8260 (mmmt) REVERT: D 78 THR cc_start: 0.8040 (m) cc_final: 0.7347 (p) outliers start: 27 outliers final: 22 residues processed: 411 average time/residue: 0.2825 time to fit residues: 158.0830 Evaluate side-chains 427 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 403 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1109 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1165 LYS Chi-restraints excluded: chain B residue 1215 ASN Chi-restraints excluded: chain B residue 1331 LEU Chi-restraints excluded: chain B residue 1389 MET Chi-restraints excluded: chain C residue 1505 THR Chi-restraints excluded: chain C residue 1565 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 58 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 115 optimal weight: 0.0670 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.125767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110234 restraints weight = 53735.822| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.81 r_work: 0.3334 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11955 Z= 0.134 Angle : 0.563 7.183 16249 Z= 0.282 Chirality : 0.043 0.285 1849 Planarity : 0.004 0.064 2096 Dihedral : 6.489 90.424 1729 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.04 % Allowed : 19.81 % Favored : 78.14 % 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: -0.32 (0.22), residues: 1495 helix: 1.52 (0.33), residues: 266 sheet: -0.21 (0.22), residues: 522 loop : -0.83 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 137 TYR 0.016 0.001 TYR B1315 PHE 0.016 0.001 PHE A 82 TRP 0.019 0.001 TRP D 47 HIS 0.004 0.001 HIS B1150 Details of bonding type rmsd covalent geometry : bond 0.00303 (11942) covalent geometry : angle 0.55327 (16218) SS BOND : bond 0.00536 ( 8) SS BOND : angle 1.35623 ( 16) hydrogen bonds : bond 0.03545 ( 471) hydrogen bonds : angle 5.25759 ( 1347) link_BETA1-4 : bond 0.00059 ( 1) link_BETA1-4 : angle 1.21361 ( 3) link_NAG-ASN : bond 0.00762 ( 4) link_NAG-ASN : angle 3.63709 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 404 time to evaluate : 0.573 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: symmetry clash REVERT: A 38 SER cc_start: 0.8609 (m) cc_final: 0.8216 (p) REVERT: A 42 GLN cc_start: 0.7763 (pp30) cc_final: 0.7378 (pp30) REVERT: A 62 SER cc_start: 0.7907 (m) cc_final: 0.7388 (p) REVERT: A 116 TRP cc_start: 0.8067 (t60) cc_final: 0.7570 (t60) REVERT: A 126 ASN cc_start: 0.8392 (p0) cc_final: 0.8093 (p0) REVERT: A 233 VAL cc_start: 0.8085 (p) cc_final: 0.7860 (t) REVERT: A 244 LYS cc_start: 0.8399 (ptpt) cc_final: 0.8145 (ptpp) REVERT: A 282 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8456 (m) REVERT: A 300 GLU cc_start: 0.8035 (mp0) cc_final: 0.7833 (mp0) REVERT: A 304 LYS cc_start: 0.8697 (ttpp) cc_final: 0.8380 (ttpp) REVERT: A 404 LYS cc_start: 0.7972 (mmmt) cc_final: 0.7689 (mttm) REVERT: A 521 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7135 (mm-30) REVERT: A 629 ASN cc_start: 0.8191 (t0) cc_final: 0.7957 (t0) REVERT: A 642 SER cc_start: 0.8073 (m) cc_final: 0.7727 (p) REVERT: A 667 LEU cc_start: 0.8226 (mp) cc_final: 0.7990 (tp) REVERT: B 801 ASP cc_start: 0.7773 (m-30) cc_final: 0.7510 (m-30) REVERT: B 815 LYS cc_start: 0.8600 (mttp) cc_final: 0.8298 (mttp) REVERT: B 889 VAL cc_start: 0.8587 (p) cc_final: 0.8368 (t) REVERT: B 923 VAL cc_start: 0.7764 (t) cc_final: 0.7283 (m) REVERT: B 941 ARG cc_start: 0.7800 (ptp-110) cc_final: 0.7557 (ptp90) REVERT: B 947 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7263 (mm-30) REVERT: B 968 MET cc_start: 0.8130 (tmm) cc_final: 0.7620 (tmm) REVERT: B 969 ILE cc_start: 0.8904 (mt) cc_final: 0.8564 (mt) REVERT: B 974 PHE cc_start: 0.7950 (t80) cc_final: 0.7638 (t80) REVERT: B 1085 VAL cc_start: 0.8597 (t) cc_final: 0.8231 (m) REVERT: B 1129 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8252 (tp40) REVERT: B 1167 ARG cc_start: 0.8323 (mtm180) cc_final: 0.8081 (ttp80) REVERT: B 1288 TRP cc_start: 0.8270 (t60) cc_final: 0.7895 (t60) REVERT: B 1358 LEU cc_start: 0.8512 (tt) cc_final: 0.8283 (tt) REVERT: B 1384 TYR cc_start: 0.8283 (p90) cc_final: 0.7962 (p90) REVERT: C 1483 MET cc_start: 0.7805 (ptp) cc_final: 0.7260 (ptp) REVERT: C 1487 ASP cc_start: 0.8063 (t0) cc_final: 0.7745 (t0) REVERT: C 1515 PHE cc_start: 0.8011 (p90) cc_final: 0.7753 (p90) REVERT: C 1523 LEU cc_start: 0.8475 (mt) cc_final: 0.8088 (mp) REVERT: C 1527 ASP cc_start: 0.7830 (p0) cc_final: 0.7540 (p0) REVERT: D 49 SER cc_start: 0.8464 (p) cc_final: 0.8226 (p) REVERT: D 76 LYS cc_start: 0.8494 (mmmt) cc_final: 0.8248 (mmmt) REVERT: D 78 THR cc_start: 0.8005 (m) cc_final: 0.7305 (p) outliers start: 26 outliers final: 22 residues processed: 414 average time/residue: 0.2906 time to fit residues: 164.3091 Evaluate side-chains 422 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 399 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1165 LYS Chi-restraints excluded: chain B residue 1331 LEU Chi-restraints excluded: chain B residue 1402 THR Chi-restraints excluded: chain C residue 1501 LEU Chi-restraints excluded: chain C residue 1505 THR Chi-restraints excluded: chain C residue 1565 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 143 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.123624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108207 restraints weight = 54024.622| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.79 r_work: 0.3263 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11955 Z= 0.261 Angle : 0.617 8.472 16249 Z= 0.316 Chirality : 0.043 0.286 1849 Planarity : 0.004 0.066 2096 Dihedral : 6.602 88.872 1729 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.20 % Allowed : 20.05 % Favored : 77.75 % 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: -0.54 (0.22), residues: 1495 helix: 1.21 (0.33), residues: 266 sheet: -0.32 (0.22), residues: 533 loop : -0.95 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 137 TYR 0.023 0.002 TYR D 105 PHE 0.023 0.002 PHE C1494 TRP 0.033 0.002 TRP D 47 HIS 0.009 0.001 HIS B1150 Details of bonding type rmsd covalent geometry : bond 0.00557 (11942) covalent geometry : angle 0.60622 (16218) SS BOND : bond 0.00619 ( 8) SS BOND : angle 1.51936 ( 16) hydrogen bonds : bond 0.04019 ( 471) hydrogen bonds : angle 5.42846 ( 1347) link_BETA1-4 : bond 0.00417 ( 1) link_BETA1-4 : angle 1.40575 ( 3) link_NAG-ASN : bond 0.00722 ( 4) link_NAG-ASN : angle 3.91054 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 397 time to evaluate : 0.632 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 38 SER cc_start: 0.8608 (m) cc_final: 0.8225 (p) REVERT: A 42 GLN cc_start: 0.7729 (pp30) cc_final: 0.7379 (pp30) REVERT: A 62 SER cc_start: 0.8000 (m) cc_final: 0.7508 (p) REVERT: A 116 TRP cc_start: 0.8165 (t60) cc_final: 0.7630 (t60) REVERT: A 126 ASN cc_start: 0.8461 (p0) cc_final: 0.8161 (p0) REVERT: A 233 VAL cc_start: 0.8162 (p) cc_final: 0.7925 (t) REVERT: A 244 LYS cc_start: 0.8412 (ptpt) cc_final: 0.8165 (ptpp) REVERT: A 282 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8495 (m) REVERT: A 304 LYS cc_start: 0.8738 (ttpp) cc_final: 0.8358 (ttmm) REVERT: A 379 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.7546 (t) REVERT: A 404 LYS cc_start: 0.7953 (mmmt) cc_final: 0.7689 (mttm) REVERT: A 521 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6887 (mm-30) REVERT: A 629 ASN cc_start: 0.8255 (t0) cc_final: 0.7985 (t0) REVERT: A 642 SER cc_start: 0.8151 (m) cc_final: 0.7819 (p) REVERT: A 667 LEU cc_start: 0.8276 (mp) cc_final: 0.8045 (tp) REVERT: B 801 ASP cc_start: 0.7761 (m-30) cc_final: 0.7532 (m-30) REVERT: B 815 LYS cc_start: 0.8590 (mttp) cc_final: 0.8276 (mttp) REVERT: B 889 VAL cc_start: 0.8623 (p) cc_final: 0.8405 (t) REVERT: B 923 VAL cc_start: 0.7823 (t) cc_final: 0.7346 (m) REVERT: B 941 ARG cc_start: 0.7816 (ptp-110) cc_final: 0.7610 (ptp90) REVERT: B 947 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7260 (mm-30) REVERT: B 968 MET cc_start: 0.8096 (tmm) cc_final: 0.7575 (tmm) REVERT: B 969 ILE cc_start: 0.8927 (mt) cc_final: 0.8580 (mt) REVERT: B 974 PHE cc_start: 0.7939 (t80) cc_final: 0.7663 (t80) REVERT: B 1050 GLN cc_start: 0.8040 (tp40) cc_final: 0.7709 (tp40) REVERT: B 1085 VAL cc_start: 0.8695 (t) cc_final: 0.8324 (m) REVERT: B 1129 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8238 (tp40) REVERT: B 1162 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7356 (mp0) REVERT: B 1167 ARG cc_start: 0.8311 (mtm180) cc_final: 0.8054 (ttp80) REVERT: B 1174 LYS cc_start: 0.8686 (tttt) cc_final: 0.8314 (tttp) REVERT: B 1288 TRP cc_start: 0.8347 (t60) cc_final: 0.7978 (t60) REVERT: B 1303 GLN cc_start: 0.8069 (tp40) cc_final: 0.7826 (tp40) REVERT: B 1380 VAL cc_start: 0.8405 (m) cc_final: 0.8111 (t) REVERT: B 1384 TYR cc_start: 0.8311 (p90) cc_final: 0.8025 (p90) REVERT: C 1483 MET cc_start: 0.7865 (ptp) cc_final: 0.7245 (ptp) REVERT: C 1487 ASP cc_start: 0.7994 (t0) cc_final: 0.7750 (t0) REVERT: C 1515 PHE cc_start: 0.8095 (p90) cc_final: 0.7841 (p90) REVERT: C 1527 ASP cc_start: 0.7801 (p0) cc_final: 0.7537 (p0) REVERT: C 1541 VAL cc_start: 0.7724 (OUTLIER) cc_final: 0.7501 (m) REVERT: D 49 SER cc_start: 0.8545 (p) cc_final: 0.8310 (p) REVERT: D 76 LYS cc_start: 0.8495 (mmmt) cc_final: 0.8273 (mmmt) REVERT: D 78 THR cc_start: 0.7892 (m) cc_final: 0.7192 (p) outliers start: 28 outliers final: 22 residues processed: 407 average time/residue: 0.2852 time to fit residues: 158.1567 Evaluate side-chains 421 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 396 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1331 LEU Chi-restraints excluded: chain B residue 1402 THR Chi-restraints excluded: chain C residue 1505 THR Chi-restraints excluded: chain C residue 1541 VAL Chi-restraints excluded: chain C residue 1565 ARG Chi-restraints excluded: chain C residue 1582 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 133 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 143 optimal weight: 0.0870 chunk 1 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.124942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.109418 restraints weight = 53758.182| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.83 r_work: 0.3354 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11955 Z= 0.145 Angle : 0.579 7.184 16249 Z= 0.290 Chirality : 0.043 0.288 1849 Planarity : 0.004 0.064 2096 Dihedral : 6.454 88.858 1729 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.65 % Allowed : 20.83 % Favored : 77.52 % 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: -0.40 (0.22), residues: 1495 helix: 1.46 (0.33), residues: 266 sheet: -0.26 (0.22), residues: 517 loop : -0.87 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 137 TYR 0.018 0.001 TYR B1315 PHE 0.018 0.001 PHE C1494 TRP 0.023 0.001 TRP D 47 HIS 0.005 0.001 HIS B1342 Details of bonding type rmsd covalent geometry : bond 0.00322 (11942) covalent geometry : angle 0.56845 (16218) SS BOND : bond 0.00545 ( 8) SS BOND : angle 1.49725 ( 16) hydrogen bonds : bond 0.03564 ( 471) hydrogen bonds : angle 5.21468 ( 1347) link_BETA1-4 : bond 0.00058 ( 1) link_BETA1-4 : angle 1.25928 ( 3) link_NAG-ASN : bond 0.00761 ( 4) link_NAG-ASN : angle 3.68327 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 400 time to evaluate : 0.609 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: A 38 SER cc_start: 0.8608 (m) cc_final: 0.8225 (p) REVERT: A 42 GLN cc_start: 0.7766 (pp30) cc_final: 0.7405 (pp30) REVERT: A 62 SER cc_start: 0.7966 (m) cc_final: 0.7465 (p) REVERT: A 116 TRP cc_start: 0.8049 (t60) cc_final: 0.7507 (t60) REVERT: A 126 ASN cc_start: 0.8445 (p0) cc_final: 0.8133 (p0) REVERT: A 233 VAL cc_start: 0.8046 (p) cc_final: 0.7830 (t) REVERT: A 244 LYS cc_start: 0.8410 (ptpt) cc_final: 0.7995 (ptpp) REVERT: A 282 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8462 (m) REVERT: A 304 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8322 (ttmm) REVERT: A 404 LYS cc_start: 0.7891 (mmmt) cc_final: 0.7628 (mttm) REVERT: A 521 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6869 (mm-30) REVERT: A 629 ASN cc_start: 0.8221 (t0) cc_final: 0.7933 (t0) REVERT: A 642 SER cc_start: 0.8092 (m) cc_final: 0.7735 (p) REVERT: A 667 LEU cc_start: 0.8264 (mp) cc_final: 0.8031 (tp) REVERT: B 801 ASP cc_start: 0.7789 (m-30) cc_final: 0.7521 (m-30) REVERT: B 815 LYS cc_start: 0.8591 (mttp) cc_final: 0.8298 (mttp) REVERT: B 889 VAL cc_start: 0.8615 (p) cc_final: 0.8401 (t) REVERT: B 923 VAL cc_start: 0.7767 (t) cc_final: 0.7303 (m) REVERT: B 947 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7282 (mm-30) REVERT: B 968 MET cc_start: 0.8099 (tmm) cc_final: 0.7566 (tmm) REVERT: B 969 ILE cc_start: 0.8922 (mt) cc_final: 0.8575 (mt) REVERT: B 974 PHE cc_start: 0.7931 (t80) cc_final: 0.7639 (t80) REVERT: B 1050 GLN cc_start: 0.7970 (tp40) cc_final: 0.7633 (tp40) REVERT: B 1085 VAL cc_start: 0.8608 (t) cc_final: 0.8240 (m) REVERT: B 1129 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8253 (tp40) REVERT: B 1167 ARG cc_start: 0.8259 (mtm180) cc_final: 0.7957 (ttp80) REVERT: B 1174 LYS cc_start: 0.8665 (tttt) cc_final: 0.8287 (tttp) REVERT: B 1288 TRP cc_start: 0.8282 (t60) cc_final: 0.7998 (t60) REVERT: B 1380 VAL cc_start: 0.8358 (m) cc_final: 0.8075 (t) REVERT: B 1384 TYR cc_start: 0.8289 (p90) cc_final: 0.8002 (p90) REVERT: C 1483 MET cc_start: 0.7766 (ptp) cc_final: 0.7191 (ptp) REVERT: C 1487 ASP cc_start: 0.8047 (t0) cc_final: 0.7814 (t0) REVERT: C 1527 ASP cc_start: 0.7785 (p0) cc_final: 0.7490 (p0) REVERT: C 1541 VAL cc_start: 0.7762 (t) cc_final: 0.7561 (m) REVERT: D 49 SER cc_start: 0.8486 (p) cc_final: 0.8236 (p) REVERT: D 76 LYS cc_start: 0.8481 (mmmt) cc_final: 0.8250 (mmmt) REVERT: D 78 THR cc_start: 0.7867 (m) cc_final: 0.7179 (p) outliers start: 21 outliers final: 18 residues processed: 409 average time/residue: 0.2960 time to fit residues: 164.8671 Evaluate side-chains 415 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 396 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 199 GLN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1331 LEU Chi-restraints excluded: chain C residue 1501 LEU Chi-restraints excluded: chain C residue 1505 THR Chi-restraints excluded: chain C residue 1565 ARG Chi-restraints excluded: chain C residue 1582 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 64 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 119 optimal weight: 0.0370 chunk 129 optimal weight: 0.0470 chunk 94 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 39 optimal weight: 0.2980 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.126547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.111104 restraints weight = 53582.202| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.80 r_work: 0.3367 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11955 Z= 0.112 Angle : 0.569 7.234 16249 Z= 0.283 Chirality : 0.043 0.289 1849 Planarity : 0.004 0.073 2096 Dihedral : 6.305 88.291 1729 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.57 % Allowed : 21.62 % Favored : 76.81 % 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: -0.25 (0.22), residues: 1495 helix: 1.62 (0.33), residues: 266 sheet: -0.20 (0.22), residues: 517 loop : -0.78 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 137 TYR 0.018 0.001 TYR B1315 PHE 0.017 0.001 PHE D 102 TRP 0.018 0.001 TRP D 47 HIS 0.003 0.001 HIS B1342 Details of bonding type rmsd covalent geometry : bond 0.00260 (11942) covalent geometry : angle 0.55954 (16218) SS BOND : bond 0.00469 ( 8) SS BOND : angle 1.37683 ( 16) hydrogen bonds : bond 0.03298 ( 471) hydrogen bonds : angle 5.04678 ( 1347) link_BETA1-4 : bond 0.00175 ( 1) link_BETA1-4 : angle 1.12676 ( 3) link_NAG-ASN : bond 0.00797 ( 4) link_NAG-ASN : angle 3.57390 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6126.80 seconds wall clock time: 104 minutes 24.40 seconds (6264.40 seconds total)