Starting phenix.real_space_refine on Thu May 22 20:55:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b2p_11989/05_2025/7b2p_11989_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b2p_11989/05_2025/7b2p_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7b2p_11989/05_2025/7b2p_11989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b2p_11989/05_2025/7b2p_11989.map" model { file = "/net/cci-nas-00/data/ceres_data/7b2p_11989/05_2025/7b2p_11989_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b2p_11989/05_2025/7b2p_11989_trim.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.25, per 1000 atoms: 0.44 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: 6.10 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 2.08 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: 9.34 Time building geometry restraints manager: 7.25 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: 1.810 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: 0.420 Extract box with map and model: 0.850 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 48.060 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.820 ------------------------------------------------------------------------------- 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 : 8.42 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (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 TRP 0.041 0.001 TRP D 47 HIS 0.003 0.001 HIS B1150 PHE 0.027 0.001 PHE A 74 TYR 0.008 0.001 TYR A 272 ARG 0.014 0.001 ARG B 979 Details of bonding type rmsd link_NAG-ASN : bond 0.01084 ( 4) link_NAG-ASN : angle 3.68145 ( 12) link_BETA1-4 : bond 0.00994 ( 1) link_BETA1-4 : angle 3.59135 ( 3) hydrogen bonds : bond 0.25355 ( 471) hydrogen bonds : angle 9.72970 ( 1347) SS BOND : bond 0.00157 ( 8) SS BOND : angle 0.72771 ( 16) covalent geometry : bond 0.00328 (11942) covalent geometry : angle 0.52875 (16218) *********************** 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 : 1.904 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: 0.7444 (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: 0.7993 (mttp) cc_final: 0.7715 (mttp) REVERT: B 817 LYS cc_start: 0.7982 (mmtt) cc_final: 0.7716 (mmtp) REVERT: B 910 SER cc_start: 0.7449 (t) cc_final: 0.7212 (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: 0.8359 (mt) REVERT: B 974 PHE cc_start: 0.7611 (t80) cc_final: 0.7377 (t80) REVERT: B 1085 VAL cc_start: 0.8700 (t) cc_final: 0.8426 (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: 0.7855 (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: 0.6238 (ptp) REVERT: C 1527 ASP cc_start: 0.7438 (p0) cc_final: 0.6939 (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: 0.5967 time to fit residues: 345.9994 Evaluate side-chains 370 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 60 optimal weight: 0.1980 chunk 117 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 ASN ** B1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1256 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.125026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.109475 restraints weight = 54362.744| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.79 r_work: 0.3331 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11955 Z= 0.242 Angle : 0.657 7.993 16249 Z= 0.340 Chirality : 0.045 0.250 1849 Planarity : 0.005 0.042 2096 Dihedral : 7.225 97.082 1729 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.49 % Allowed : 10.85 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.21), residues: 1495 helix: 0.94 (0.32), residues: 267 sheet: -0.39 (0.22), residues: 530 loop : -0.80 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 47 HIS 0.008 0.001 HIS B1150 PHE 0.024 0.002 PHE A 74 TYR 0.019 0.002 TYR D 105 ARG 0.005 0.001 ARG A 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00762 ( 4) link_NAG-ASN : angle 3.82781 ( 12) link_BETA1-4 : bond 0.00020 ( 1) link_BETA1-4 : angle 1.66909 ( 3) hydrogen bonds : bond 0.05393 ( 471) hydrogen bonds : angle 6.76435 ( 1347) SS BOND : bond 0.00562 ( 8) SS BOND : angle 1.48114 ( 16) covalent geometry : bond 0.00520 (11942) covalent geometry : angle 0.64681 (16218) *********************** 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 415 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 396 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8565 (m) cc_final: 0.8152 (p) REVERT: A 42 GLN cc_start: 0.8032 (pp30) cc_final: 0.7350 (pp30) REVERT: A 62 SER cc_start: 0.7741 (m) cc_final: 0.7264 (p) REVERT: A 79 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7843 (pp20) REVERT: A 121 LEU cc_start: 0.8511 (mt) cc_final: 0.8217 (mp) REVERT: A 304 LYS cc_start: 0.8766 (ttpp) cc_final: 0.8457 (ttpp) REVERT: A 352 MET cc_start: 0.8185 (ptp) cc_final: 0.7939 (ptm) REVERT: A 404 LYS cc_start: 0.8000 (mmmt) cc_final: 0.7642 (mttm) REVERT: A 433 ILE cc_start: 0.8748 (tt) cc_final: 0.8357 (pt) REVERT: A 642 SER cc_start: 0.8073 (m) cc_final: 0.7692 (p) REVERT: B 801 ASP cc_start: 0.7663 (m-30) cc_final: 0.7451 (m-30) REVERT: B 815 LYS cc_start: 0.8473 (mttp) cc_final: 0.8177 (mttp) REVERT: B 817 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7728 (mmtm) REVERT: B 942 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7073 (mm-30) REVERT: B 968 MET cc_start: 0.8187 (tmm) cc_final: 0.7791 (tmm) REVERT: B 969 ILE cc_start: 0.8854 (mt) cc_final: 0.8491 (mt) REVERT: B 974 PHE cc_start: 0.8035 (t80) cc_final: 0.7726 (t80) REVERT: B 1085 VAL cc_start: 0.8665 (t) cc_final: 0.8299 (m) REVERT: B 1229 TYR cc_start: 0.6828 (m-80) cc_final: 0.6563 (m-80) REVERT: B 1288 TRP cc_start: 0.8384 (t60) cc_final: 0.7978 (t60) REVERT: B 1384 TYR cc_start: 0.8203 (p90) cc_final: 0.7739 (p90) REVERT: C 1483 MET cc_start: 0.7664 (ptp) cc_final: 0.6872 (ptp) REVERT: C 1515 PHE cc_start: 0.7943 (p90) cc_final: 0.7703 (p90) REVERT: C 1523 LEU cc_start: 0.8417 (mt) cc_final: 0.8111 (mp) REVERT: C 1527 ASP cc_start: 0.7708 (p0) cc_final: 0.7308 (p0) REVERT: D 78 THR cc_start: 0.8093 (m) cc_final: 0.7652 (p) REVERT: D 83 MET cc_start: 0.8121 (mpp) cc_final: 0.7858 (mpp) outliers start: 19 outliers final: 11 residues processed: 399 average time/residue: 0.6111 time to fit residues: 332.7633 Evaluate side-chains 403 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 391 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU 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 488 THR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 142 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 199 GLN ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1227 ASN B1256 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.122106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.106176 restraints weight = 54606.295| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.85 r_work: 0.3289 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11955 Z= 0.185 Angle : 0.588 7.380 16249 Z= 0.302 Chirality : 0.044 0.265 1849 Planarity : 0.004 0.043 2096 Dihedral : 7.019 95.605 1729 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.04 % Allowed : 13.13 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.21), residues: 1495 helix: 1.01 (0.32), residues: 267 sheet: -0.27 (0.22), residues: 509 loop : -0.80 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 47 HIS 0.007 0.001 HIS A 535 PHE 0.017 0.001 PHE C1494 TYR 0.018 0.001 TYR D 105 ARG 0.005 0.000 ARG A 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00718 ( 4) link_NAG-ASN : angle 3.63586 ( 12) link_BETA1-4 : bond 0.00162 ( 1) link_BETA1-4 : angle 1.49444 ( 3) hydrogen bonds : bond 0.04658 ( 471) hydrogen bonds : angle 6.15283 ( 1347) SS BOND : bond 0.00740 ( 8) SS BOND : angle 1.41732 ( 16) covalent geometry : bond 0.00401 (11942) covalent geometry : angle 0.57817 (16218) *********************** 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 432 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 406 time to evaluate : 1.732 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: 0.8590 (m) cc_final: 0.8176 (p) REVERT: A 62 SER cc_start: 0.7806 (m) cc_final: 0.7273 (p) REVERT: A 116 TRP cc_start: 0.8149 (t60) cc_final: 0.7740 (t60) REVERT: A 262 MET cc_start: 0.7941 (mpp) cc_final: 0.7689 (mpp) REVERT: A 282 VAL cc_start: 0.8899 (t) cc_final: 0.8487 (m) REVERT: A 421 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8512 (mm) REVERT: A 433 ILE cc_start: 0.8743 (tt) cc_final: 0.8374 (pt) REVERT: A 642 SER cc_start: 0.8086 (m) cc_final: 0.7710 (p) REVERT: B 815 LYS cc_start: 0.8535 (mttp) cc_final: 0.8249 (mttp) REVERT: B 844 ARG cc_start: 0.7707 (tpp80) cc_final: 0.7393 (mpp80) REVERT: B 942 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7477 (mm-30) REVERT: B 968 MET cc_start: 0.8208 (tmm) cc_final: 0.7696 (tmm) REVERT: B 969 ILE cc_start: 0.8874 (mt) cc_final: 0.8514 (mt) REVERT: B 974 PHE cc_start: 0.8067 (t80) cc_final: 0.7789 (t80) REVERT: B 1005 ARG cc_start: 0.8190 (mtm180) cc_final: 0.7906 (mtt90) REVERT: B 1085 VAL cc_start: 0.8654 (t) cc_final: 0.8311 (m) REVERT: B 1129 GLN cc_start: 0.8409 (mm-40) cc_final: 0.7845 (tp40) REVERT: B 1229 TYR cc_start: 0.6849 (m-80) cc_final: 0.6487 (m-80) REVERT: B 1288 TRP cc_start: 0.8328 (t60) cc_final: 0.7862 (t60) REVERT: B 1303 GLN cc_start: 0.8004 (tp40) cc_final: 0.7732 (tp40) REVERT: B 1348 ASN cc_start: 0.6661 (t0) cc_final: 0.5824 (t0) REVERT: B 1384 TYR cc_start: 0.8254 (p90) cc_final: 0.7966 (p90) REVERT: C 1483 MET cc_start: 0.7720 (ptp) cc_final: 0.6962 (ptp) REVERT: C 1523 LEU cc_start: 0.8444 (mt) cc_final: 0.8115 (mp) REVERT: C 1527 ASP cc_start: 0.7775 (p0) cc_final: 0.7423 (p0) REVERT: D 76 LYS cc_start: 0.8561 (mmmt) cc_final: 0.8343 (mmmt) REVERT: D 78 THR cc_start: 0.8235 (m) cc_final: 0.7630 (p) outliers start: 26 outliers final: 15 residues processed: 413 average time/residue: 0.6309 time to fit residues: 356.1833 Evaluate side-chains 407 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 391 time to evaluate : 1.846 ------------------------------------------------------------------------------- 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 488 THR Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1141 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 53 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** B1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.121433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.105566 restraints weight = 55125.067| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.93 r_work: 0.3232 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 11955 Z= 0.304 Angle : 0.639 7.684 16249 Z= 0.334 Chirality : 0.045 0.265 1849 Planarity : 0.005 0.052 2096 Dihedral : 7.112 93.193 1729 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.59 % Allowed : 14.86 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1495 helix: 0.74 (0.32), residues: 267 sheet: -0.41 (0.22), residues: 542 loop : -0.96 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 47 HIS 0.009 0.002 HIS B1150 PHE 0.026 0.002 PHE C1494 TYR 0.023 0.002 TYR D 105 ARG 0.006 0.000 ARG A 157 Details of bonding type rmsd link_NAG-ASN : bond 0.00768 ( 4) link_NAG-ASN : angle 4.08724 ( 12) link_BETA1-4 : bond 0.00217 ( 1) link_BETA1-4 : angle 1.74563 ( 3) hydrogen bonds : bond 0.04721 ( 471) hydrogen bonds : angle 6.06208 ( 1347) SS BOND : bond 0.00757 ( 8) SS BOND : angle 1.64119 ( 16) covalent geometry : bond 0.00647 (11942) covalent geometry : angle 0.62725 (16218) *********************** 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 441 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 408 time to evaluate : 1.940 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: 0.8665 (m) cc_final: 0.8221 (p) REVERT: A 42 GLN cc_start: 0.7862 (pp30) cc_final: 0.7281 (pp30) REVERT: A 62 SER cc_start: 0.7951 (m) cc_final: 0.7440 (p) REVERT: A 79 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7784 (pp20) REVERT: A 116 TRP cc_start: 0.8151 (t60) cc_final: 0.7598 (t60) REVERT: A 262 MET cc_start: 0.7986 (mpp) cc_final: 0.7703 (mpp) REVERT: A 282 VAL cc_start: 0.8889 (OUTLIER) cc_final: 0.8479 (m) REVERT: A 404 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7644 (mttm) REVERT: A 421 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8493 (mm) REVERT: A 433 ILE cc_start: 0.8673 (tt) cc_final: 0.8294 (pt) REVERT: A 439 GLN cc_start: 0.7760 (pt0) cc_final: 0.7474 (pm20) REVERT: A 585 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7526 (mm-30) REVERT: A 642 SER cc_start: 0.8035 (m) cc_final: 0.7666 (p) REVERT: A 667 LEU cc_start: 0.8297 (mp) cc_final: 0.8055 (tp) REVERT: B 815 LYS cc_start: 0.8611 (mttp) cc_final: 0.8287 (mttp) REVERT: B 888 LEU cc_start: 0.7810 (mt) cc_final: 0.7492 (mp) REVERT: B 942 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7434 (mm-30) REVERT: B 968 MET cc_start: 0.8156 (tmm) cc_final: 0.7618 (tmm) REVERT: B 969 ILE cc_start: 0.8864 (mt) cc_final: 0.8525 (mt) REVERT: B 974 PHE cc_start: 0.8079 (t80) cc_final: 0.7787 (t80) REVERT: B 1085 VAL cc_start: 0.8718 (t) cc_final: 0.8352 (m) REVERT: B 1229 TYR cc_start: 0.6736 (m-80) cc_final: 0.6397 (m-80) REVERT: B 1288 TRP cc_start: 0.8427 (t60) cc_final: 0.7925 (t60) REVERT: B 1303 GLN cc_start: 0.8064 (tp40) cc_final: 0.7780 (tp40) REVERT: B 1317 ILE cc_start: 0.8384 (tt) cc_final: 0.8147 (tp) REVERT: B 1384 TYR cc_start: 0.8239 (p90) cc_final: 0.7788 (p90) REVERT: C 1483 MET cc_start: 0.8000 (ptp) cc_final: 0.7336 (ptp) REVERT: C 1523 LEU cc_start: 0.8479 (mt) cc_final: 0.8074 (mp) REVERT: C 1524 LEU cc_start: 0.8556 (mp) cc_final: 0.8317 (mt) REVERT: C 1527 ASP cc_start: 0.7835 (p0) cc_final: 0.7482 (p0) REVERT: D 49 SER cc_start: 0.8517 (p) cc_final: 0.8303 (p) REVERT: D 76 LYS cc_start: 0.8555 (mmmt) cc_final: 0.8287 (mmmt) REVERT: D 78 THR cc_start: 0.8048 (m) cc_final: 0.7380 (p) outliers start: 33 outliers final: 24 residues processed: 417 average time/residue: 0.6383 time to fit residues: 368.0968 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 : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU 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 404 LYS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 592 GLU 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 1141 LEU Chi-restraints excluded: chain B residue 1215 ASN Chi-restraints excluded: chain B residue 1329 VAL 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 147 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.123457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.107608 restraints weight = 54452.765| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.89 r_work: 0.3273 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11955 Z= 0.183 Angle : 0.588 7.397 16249 Z= 0.301 Chirality : 0.043 0.270 1849 Planarity : 0.004 0.053 2096 Dihedral : 6.872 93.064 1729 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.36 % Allowed : 16.90 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.21), residues: 1495 helix: 1.08 (0.32), residues: 266 sheet: -0.35 (0.22), residues: 540 loop : -0.90 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 47 HIS 0.006 0.001 HIS B1150 PHE 0.018 0.001 PHE C1494 TYR 0.017 0.002 TYR D 105 ARG 0.006 0.000 ARG A 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00729 ( 4) link_NAG-ASN : angle 3.83068 ( 12) link_BETA1-4 : bond 0.00142 ( 1) link_BETA1-4 : angle 1.48100 ( 3) hydrogen bonds : bond 0.04120 ( 471) hydrogen bonds : angle 5.73856 ( 1347) SS BOND : bond 0.00574 ( 8) SS BOND : angle 1.35067 ( 16) covalent geometry : bond 0.00397 (11942) covalent geometry : angle 0.57784 (16218) *********************** 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 428 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 398 time to evaluate : 1.794 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: 0.8653 (m) cc_final: 0.8202 (p) REVERT: A 42 GLN cc_start: 0.7823 (pp30) cc_final: 0.7296 (pp30) REVERT: A 62 SER cc_start: 0.7887 (m) cc_final: 0.7360 (p) REVERT: A 116 TRP cc_start: 0.8121 (t60) cc_final: 0.7583 (t60) REVERT: A 262 MET cc_start: 0.7984 (mpp) cc_final: 0.7689 (mpp) REVERT: A 282 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8448 (m) REVERT: A 304 LYS cc_start: 0.8746 (ttpp) cc_final: 0.8427 (ttpp) REVERT: A 379 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.7532 (t) REVERT: A 404 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7576 (mttm) REVERT: A 417 GLU cc_start: 0.7163 (tm-30) cc_final: 0.6770 (tm-30) REVERT: A 421 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8480 (mm) REVERT: A 433 ILE cc_start: 0.8671 (tt) cc_final: 0.8302 (pt) REVERT: A 439 GLN cc_start: 0.7707 (pt0) cc_final: 0.7374 (pm20) REVERT: A 642 SER cc_start: 0.7996 (m) cc_final: 0.7636 (p) REVERT: A 667 LEU cc_start: 0.8263 (mp) cc_final: 0.8019 (tp) REVERT: B 815 LYS cc_start: 0.8544 (mttp) cc_final: 0.8257 (mttp) REVERT: B 923 VAL cc_start: 0.7750 (t) cc_final: 0.7548 (t) REVERT: B 941 ARG cc_start: 0.7813 (ptp-110) cc_final: 0.7529 (ptp90) REVERT: B 942 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7375 (mm-30) REVERT: B 968 MET cc_start: 0.8138 (tmm) cc_final: 0.7598 (tmm) REVERT: B 969 ILE cc_start: 0.8899 (mt) cc_final: 0.8547 (mt) REVERT: B 974 PHE cc_start: 0.8049 (t80) cc_final: 0.7736 (t80) REVERT: B 1085 VAL cc_start: 0.8623 (t) cc_final: 0.8274 (m) REVERT: B 1174 LYS cc_start: 0.8611 (tttt) cc_final: 0.8268 (tttm) REVERT: B 1229 TYR cc_start: 0.6795 (m-80) cc_final: 0.6407 (m-80) REVERT: B 1288 TRP cc_start: 0.8373 (t60) cc_final: 0.7902 (t60) REVERT: B 1303 GLN cc_start: 0.8095 (tp40) cc_final: 0.7815 (tp40) REVERT: B 1317 ILE cc_start: 0.8335 (tt) cc_final: 0.8098 (tp) REVERT: B 1355 GLU cc_start: 0.7601 (mp0) cc_final: 0.7332 (mp0) REVERT: B 1384 TYR cc_start: 0.8231 (p90) cc_final: 0.7778 (p90) REVERT: C 1483 MET cc_start: 0.7920 (ptp) cc_final: 0.7222 (ptp) REVERT: C 1515 PHE cc_start: 0.8033 (p90) cc_final: 0.7760 (p90) REVERT: C 1523 LEU cc_start: 0.8424 (mt) cc_final: 0.8123 (mp) REVERT: C 1527 ASP cc_start: 0.7801 (p0) cc_final: 0.7489 (p0) REVERT: D 49 SER cc_start: 0.8479 (p) cc_final: 0.8253 (p) REVERT: D 76 LYS cc_start: 0.8535 (mmmt) cc_final: 0.8272 (mmmt) REVERT: D 78 THR cc_start: 0.8018 (m) cc_final: 0.7384 (p) outliers start: 30 outliers final: 25 residues processed: 409 average time/residue: 0.6043 time to fit residues: 340.4539 Evaluate side-chains 417 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 388 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 79 GLU 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 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 346 GLU 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 404 LYS 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 A residue 508 MET Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1215 ASN Chi-restraints excluded: chain B residue 1329 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 129 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 147 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** B1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.124617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.109153 restraints weight = 54018.796| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.81 r_work: 0.3327 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11955 Z= 0.167 Angle : 0.576 7.360 16249 Z= 0.292 Chirality : 0.043 0.277 1849 Planarity : 0.004 0.056 2096 Dihedral : 6.718 92.651 1729 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.36 % Allowed : 17.37 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.21), residues: 1495 helix: 1.30 (0.33), residues: 266 sheet: -0.30 (0.22), residues: 532 loop : -0.87 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 47 HIS 0.007 0.001 HIS B1342 PHE 0.017 0.001 PHE C1494 TYR 0.017 0.001 TYR D 105 ARG 0.007 0.000 ARG A 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00734 ( 4) link_NAG-ASN : angle 3.78637 ( 12) link_BETA1-4 : bond 0.00066 ( 1) link_BETA1-4 : angle 1.31345 ( 3) hydrogen bonds : bond 0.03865 ( 471) hydrogen bonds : angle 5.52575 ( 1347) SS BOND : bond 0.00483 ( 8) SS BOND : angle 1.26142 ( 16) covalent geometry : bond 0.00369 (11942) covalent geometry : angle 0.56541 (16218) *********************** 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 426 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 396 time to evaluate : 1.761 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: 0.8622 (m) cc_final: 0.8225 (p) REVERT: A 42 GLN cc_start: 0.7767 (pp30) cc_final: 0.7333 (pp30) REVERT: A 43 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7476 (mt) REVERT: A 62 SER cc_start: 0.7866 (m) cc_final: 0.7345 (p) REVERT: A 116 TRP cc_start: 0.8144 (t60) cc_final: 0.7617 (t60) REVERT: A 126 ASN cc_start: 0.8425 (p0) cc_final: 0.8194 (p0) REVERT: A 233 VAL cc_start: 0.8081 (p) cc_final: 0.7853 (t) REVERT: A 242 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7226 (tm-30) REVERT: A 262 MET cc_start: 0.8033 (mpp) cc_final: 0.7724 (mpp) REVERT: A 282 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8465 (m) REVERT: A 304 LYS cc_start: 0.8737 (ttpp) cc_final: 0.8330 (ttmm) REVERT: A 379 VAL cc_start: 0.8344 (OUTLIER) cc_final: 0.7576 (t) REVERT: A 404 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7657 (mttm) REVERT: A 422 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7793 (tm-30) REVERT: A 433 ILE cc_start: 0.8715 (tt) cc_final: 0.8364 (pt) REVERT: A 439 GLN cc_start: 0.7686 (pt0) cc_final: 0.7436 (pm20) REVERT: A 521 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7031 (mm-30) REVERT: A 642 SER cc_start: 0.8099 (m) cc_final: 0.7759 (p) REVERT: A 648 GLN cc_start: 0.8506 (tt0) cc_final: 0.8301 (tt0) REVERT: A 667 LEU cc_start: 0.8254 (mp) cc_final: 0.8015 (tp) REVERT: B 815 LYS cc_start: 0.8564 (mttp) cc_final: 0.8279 (mttp) REVERT: B 923 VAL cc_start: 0.7790 (t) cc_final: 0.7276 (m) REVERT: B 941 ARG cc_start: 0.7820 (ptp-110) cc_final: 0.7535 (ptp90) REVERT: B 942 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7369 (mm-30) REVERT: B 947 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7205 (mm-30) REVERT: B 968 MET cc_start: 0.8109 (tmm) cc_final: 0.7597 (tmm) REVERT: B 969 ILE cc_start: 0.8882 (mt) cc_final: 0.8525 (mt) REVERT: B 974 PHE cc_start: 0.7973 (t80) cc_final: 0.7689 (t80) REVERT: B 1085 VAL cc_start: 0.8651 (t) cc_final: 0.8301 (m) REVERT: B 1129 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7904 (tp40) REVERT: B 1167 ARG cc_start: 0.8302 (mtm180) cc_final: 0.8070 (ttp80) REVERT: B 1174 LYS cc_start: 0.8642 (tttt) cc_final: 0.8263 (tptt) REVERT: B 1218 MET cc_start: 0.8133 (mmm) cc_final: 0.7906 (tpp) REVERT: B 1229 TYR cc_start: 0.6800 (m-80) cc_final: 0.6365 (m-80) REVERT: B 1288 TRP cc_start: 0.8333 (t60) cc_final: 0.7920 (t60) REVERT: B 1303 GLN cc_start: 0.8157 (tp40) cc_final: 0.7885 (tp40) REVERT: B 1317 ILE cc_start: 0.8393 (tt) cc_final: 0.8159 (tp) REVERT: B 1384 TYR cc_start: 0.8297 (p90) cc_final: 0.7820 (p90) REVERT: C 1483 MET cc_start: 0.7848 (ptp) cc_final: 0.7189 (ptp) REVERT: C 1515 PHE cc_start: 0.8025 (p90) cc_final: 0.7772 (p90) REVERT: C 1523 LEU cc_start: 0.8452 (mt) cc_final: 0.8097 (mp) REVERT: C 1527 ASP cc_start: 0.7797 (p0) cc_final: 0.7513 (p0) REVERT: D 49 SER cc_start: 0.8493 (p) cc_final: 0.8250 (p) REVERT: D 76 LYS cc_start: 0.8503 (mmmt) cc_final: 0.8262 (mmmt) REVERT: D 78 THR cc_start: 0.8082 (m) cc_final: 0.7424 (p) outliers start: 30 outliers final: 20 residues processed: 408 average time/residue: 0.5932 time to fit residues: 331.7014 Evaluate side-chains 416 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 392 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU 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 346 GLU 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 404 LYS Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 596 LEU 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 1215 ASN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 95 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.122524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.107419 restraints weight = 54150.263| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.71 r_work: 0.3254 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11955 Z= 0.259 Angle : 0.611 7.510 16249 Z= 0.314 Chirality : 0.043 0.277 1849 Planarity : 0.004 0.056 2096 Dihedral : 6.787 91.828 1729 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.28 % Allowed : 18.40 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.21), residues: 1495 helix: 1.08 (0.32), residues: 266 sheet: -0.29 (0.22), residues: 516 loop : -1.01 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 47 HIS 0.008 0.001 HIS B1150 PHE 0.021 0.002 PHE C1494 TYR 0.022 0.002 TYR D 105 ARG 0.007 0.000 ARG A 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00724 ( 4) link_NAG-ASN : angle 3.96424 ( 12) link_BETA1-4 : bond 0.00047 ( 1) link_BETA1-4 : angle 1.56235 ( 3) hydrogen bonds : bond 0.04200 ( 471) hydrogen bonds : angle 5.59119 ( 1347) SS BOND : bond 0.00795 ( 8) SS BOND : angle 1.58016 ( 16) covalent geometry : bond 0.00555 (11942) covalent geometry : angle 0.59979 (16218) *********************** 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 427 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 398 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8602 (m) cc_final: 0.8224 (p) REVERT: A 42 GLN cc_start: 0.7707 (pp30) cc_final: 0.7308 (pp30) REVERT: A 43 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7508 (mt) REVERT: A 62 SER cc_start: 0.7947 (m) cc_final: 0.7467 (p) REVERT: A 116 TRP cc_start: 0.8204 (t60) cc_final: 0.7639 (t60) REVERT: A 126 ASN cc_start: 0.8484 (p0) cc_final: 0.8236 (p0) REVERT: A 233 VAL cc_start: 0.8114 (p) cc_final: 0.7895 (t) REVERT: A 242 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7268 (tm-30) REVERT: A 262 MET cc_start: 0.8033 (mpp) cc_final: 0.7749 (mpp) REVERT: A 282 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8481 (m) REVERT: A 304 LYS cc_start: 0.8734 (ttpp) cc_final: 0.8374 (ttmm) REVERT: A 346 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: A 379 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.7583 (t) REVERT: A 404 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7689 (mttm) REVERT: A 433 ILE cc_start: 0.8669 (tt) cc_final: 0.8317 (pt) REVERT: A 521 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7093 (mm-30) REVERT: A 642 SER cc_start: 0.8195 (m) cc_final: 0.7847 (p) REVERT: A 667 LEU cc_start: 0.8304 (mp) cc_final: 0.8067 (tp) REVERT: B 815 LYS cc_start: 0.8556 (mttp) cc_final: 0.8252 (mttp) REVERT: B 845 ARG cc_start: 0.7436 (ptm160) cc_final: 0.7179 (ptm-80) REVERT: B 923 VAL cc_start: 0.7832 (t) cc_final: 0.7346 (m) REVERT: B 947 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7247 (mm-30) REVERT: B 968 MET cc_start: 0.8096 (tmm) cc_final: 0.7584 (tmm) REVERT: B 969 ILE cc_start: 0.8900 (mt) cc_final: 0.8556 (mt) REVERT: B 974 PHE cc_start: 0.7974 (t80) cc_final: 0.7692 (t80) REVERT: B 1050 GLN cc_start: 0.8086 (tp40) cc_final: 0.7757 (tp40) REVERT: B 1085 VAL cc_start: 0.8686 (t) cc_final: 0.8327 (m) REVERT: B 1129 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8206 (tp40) REVERT: B 1167 ARG cc_start: 0.8280 (mtm180) cc_final: 0.8070 (ttp80) REVERT: B 1174 LYS cc_start: 0.8661 (tttt) cc_final: 0.8268 (tttp) REVERT: B 1229 TYR cc_start: 0.6782 (m-80) cc_final: 0.6328 (m-80) REVERT: B 1288 TRP cc_start: 0.8382 (t60) cc_final: 0.8003 (t60) REVERT: B 1303 GLN cc_start: 0.8087 (tp40) cc_final: 0.7828 (tp40) REVERT: B 1317 ILE cc_start: 0.8451 (tt) cc_final: 0.8210 (tp) REVERT: B 1358 LEU cc_start: 0.8467 (tt) cc_final: 0.8246 (tt) REVERT: B 1384 TYR cc_start: 0.8325 (p90) cc_final: 0.7811 (p90) REVERT: C 1483 MET cc_start: 0.7908 (ptp) cc_final: 0.7310 (ptp) REVERT: C 1515 PHE cc_start: 0.8083 (p90) cc_final: 0.7818 (p90) REVERT: C 1527 ASP cc_start: 0.7826 (p0) cc_final: 0.7559 (p0) REVERT: D 49 SER cc_start: 0.8511 (p) cc_final: 0.8269 (p) REVERT: D 76 LYS cc_start: 0.8499 (mmmt) cc_final: 0.8290 (mmmt) REVERT: D 78 THR cc_start: 0.8070 (m) cc_final: 0.7386 (p) outliers start: 29 outliers final: 20 residues processed: 411 average time/residue: 0.6141 time to fit residues: 348.0708 Evaluate side-chains 418 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 393 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU 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 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 346 GLU 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 404 LYS Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1215 ASN 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 97 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 147 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 88 optimal weight: 0.2980 chunk 123 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.124239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109078 restraints weight = 54001.644| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.71 r_work: 0.3281 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11955 Z= 0.158 Angle : 0.580 7.344 16249 Z= 0.294 Chirality : 0.043 0.282 1849 Planarity : 0.004 0.065 2096 Dihedral : 6.634 91.843 1729 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.89 % Allowed : 19.73 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.22), residues: 1495 helix: 1.36 (0.33), residues: 266 sheet: -0.23 (0.22), residues: 517 loop : -0.93 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 47 HIS 0.005 0.001 HIS B1150 PHE 0.018 0.001 PHE C1494 TYR 0.016 0.001 TYR B1315 ARG 0.009 0.000 ARG A 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00746 ( 4) link_NAG-ASN : angle 3.80540 ( 12) link_BETA1-4 : bond 0.00071 ( 1) link_BETA1-4 : angle 1.25630 ( 3) hydrogen bonds : bond 0.03779 ( 471) hydrogen bonds : angle 5.37001 ( 1347) SS BOND : bond 0.00438 ( 8) SS BOND : angle 1.45017 ( 16) covalent geometry : bond 0.00348 (11942) covalent geometry : angle 0.56903 (16218) *********************** 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 422 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 398 time to evaluate : 1.718 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: 0.8578 (m) cc_final: 0.8199 (p) REVERT: A 42 GLN cc_start: 0.7678 (pp30) cc_final: 0.7308 (pp30) REVERT: A 62 SER cc_start: 0.7944 (m) cc_final: 0.7452 (p) REVERT: A 116 TRP cc_start: 0.8099 (t60) cc_final: 0.7497 (t60) REVERT: A 233 VAL cc_start: 0.8001 (p) cc_final: 0.7773 (t) REVERT: A 242 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7258 (tm-30) REVERT: A 262 MET cc_start: 0.8007 (mpp) cc_final: 0.7711 (mpp) REVERT: A 282 VAL cc_start: 0.8848 (OUTLIER) cc_final: 0.8473 (m) REVERT: A 304 LYS cc_start: 0.8714 (ttpp) cc_final: 0.8377 (ttmm) REVERT: A 379 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.7587 (t) REVERT: A 404 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7603 (mttm) REVERT: A 422 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7843 (tm-30) REVERT: A 433 ILE cc_start: 0.8713 (tt) cc_final: 0.8389 (pt) REVERT: A 521 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7002 (mm-30) REVERT: A 642 SER cc_start: 0.8177 (m) cc_final: 0.7840 (p) REVERT: A 667 LEU cc_start: 0.8291 (mp) cc_final: 0.8052 (tp) REVERT: B 815 LYS cc_start: 0.8597 (mttp) cc_final: 0.8304 (mttp) REVERT: B 845 ARG cc_start: 0.7395 (ptm160) cc_final: 0.7137 (ptm-80) REVERT: B 923 VAL cc_start: 0.7800 (t) cc_final: 0.7341 (m) REVERT: B 941 ARG cc_start: 0.7789 (ptp-110) cc_final: 0.7557 (ptp90) REVERT: B 947 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7268 (mm-30) REVERT: B 968 MET cc_start: 0.8067 (tmm) cc_final: 0.7549 (tmm) REVERT: B 969 ILE cc_start: 0.8910 (mt) cc_final: 0.8559 (mt) REVERT: B 974 PHE cc_start: 0.7935 (t80) cc_final: 0.7635 (t80) REVERT: B 1050 GLN cc_start: 0.8059 (tp40) cc_final: 0.7703 (tp40) REVERT: B 1085 VAL cc_start: 0.8653 (t) cc_final: 0.8297 (m) REVERT: B 1129 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8202 (tp40) REVERT: B 1288 TRP cc_start: 0.8328 (t60) cc_final: 0.7989 (t60) REVERT: B 1303 GLN cc_start: 0.8062 (tp40) cc_final: 0.7796 (tp40) REVERT: B 1317 ILE cc_start: 0.8423 (tt) cc_final: 0.8181 (tp) REVERT: B 1358 LEU cc_start: 0.8455 (tt) cc_final: 0.8244 (tt) REVERT: B 1384 TYR cc_start: 0.8316 (p90) cc_final: 0.7811 (p90) REVERT: C 1483 MET cc_start: 0.7863 (ptp) cc_final: 0.7261 (ptp) REVERT: C 1515 PHE cc_start: 0.8061 (p90) cc_final: 0.7809 (p90) REVERT: C 1527 ASP cc_start: 0.7859 (p0) cc_final: 0.7595 (p0) REVERT: D 49 SER cc_start: 0.8483 (p) cc_final: 0.8238 (p) REVERT: D 76 LYS cc_start: 0.8486 (mmmt) cc_final: 0.8271 (mmmt) REVERT: D 78 THR cc_start: 0.7959 (m) cc_final: 0.7278 (p) REVERT: D 95 SER cc_start: 0.8389 (p) cc_final: 0.8115 (p) outliers start: 24 outliers final: 19 residues processed: 407 average time/residue: 0.6349 time to fit residues: 357.4572 Evaluate side-chains 410 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 388 time to evaluate : 1.922 ------------------------------------------------------------------------------- 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 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 346 GLU 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 404 LYS Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1215 ASN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.4612 > 50: distance: 154 - 190: 13.110 distance: 160 - 200: 12.797 distance: 168 - 210: 12.558 distance: 182 - 190: 11.701 distance: 183 - 229: 6.468 distance: 190 - 191: 3.158 distance: 190 - 195: 3.813 distance: 191 - 192: 6.554 distance: 191 - 194: 9.845 distance: 191 - 196: 8.097 distance: 192 - 193: 3.419 distance: 192 - 200: 4.152 distance: 193 - 243: 9.481 distance: 194 - 197: 7.344 distance: 194 - 198: 6.216 distance: 194 - 199: 8.524 distance: 200 - 201: 5.168 distance: 200 - 205: 16.812 distance: 201 - 202: 13.007 distance: 201 - 204: 8.319 distance: 201 - 206: 8.623 distance: 202 - 203: 11.654 distance: 202 - 210: 14.794 distance: 204 - 207: 9.188 distance: 204 - 208: 7.502 distance: 204 - 209: 7.637 distance: 210 - 211: 12.295 distance: 210 - 218: 10.535 distance: 211 - 212: 9.393 distance: 211 - 214: 8.703 distance: 211 - 219: 13.048 distance: 212 - 213: 11.345 distance: 212 - 229: 11.454 distance: 213 - 274: 14.217 distance: 214 - 215: 10.435 distance: 214 - 216: 6.913 distance: 215 - 217: 5.740 distance: 215 - 221: 8.951 distance: 215 - 222: 11.328 distance: 216 - 223: 12.034 distance: 216 - 224: 6.026 distance: 216 - 225: 5.099 distance: 217 - 226: 3.710 distance: 217 - 227: 6.442 distance: 217 - 228: 3.009 distance: 229 - 236: 13.581 distance: 230 - 231: 7.862 distance: 230 - 237: 14.903 distance: 231 - 232: 7.018 distance: 231 - 243: 14.113 distance: 232 - 284: 4.454 distance: 233 - 234: 5.507 distance: 233 - 235: 12.244 distance: 233 - 238: 7.129 distance: 234 - 239: 18.221 distance: 235 - 240: 8.559 distance: 235 - 241: 3.560 distance: 243 - 244: 14.414 distance: 243 - 248: 15.975 distance: 244 - 245: 8.914 distance: 244 - 247: 10.576 distance: 244 - 249: 3.580 distance: 245 - 246: 18.212 distance: 245 - 253: 9.899 distance: 246 - 303: 18.169 distance: 247 - 250: 9.079 distance: 247 - 251: 6.369 distance: 247 - 252: 7.684 distance: 253 - 254: 6.989 distance: 253 - 265: 14.834 distance: 254 - 255: 14.645 distance: 254 - 257: 5.328 distance: 254 - 266: 4.100 distance: 255 - 256: 10.608 distance: 255 - 274: 18.902 distance: 256 - 314: 32.174 distance: 257 - 258: 7.084 distance: 257 - 267: 5.455 distance: 257 - 268: 13.638 distance: 258 - 259: 3.356 distance: 259 - 261: 4.993 distance: 260 - 262: 3.613 distance: 260 - 270: 3.129 distance: 261 - 263: 5.137 distance: 263 - 264: 7.306 distance: 264 - 273: 5.491 distance: 274 - 275: 10.069 distance: 274 - 279: 7.536 distance: 275 - 276: 18.515 distance: 275 - 278: 14.509 distance: 275 - 280: 8.337 distance: 276 - 277: 17.075 distance: 276 - 284: 13.866 distance: 277 - 333: 9.430 distance: 278 - 281: 9.232 distance: 278 - 282: 6.897 distance: 278 - 283: 13.570 distance: 284 - 285: 14.947 distance: 284 - 292: 18.817 distance: 285 - 286: 17.083 distance: 285 - 288: 22.053 distance: 285 - 293: 22.848 distance: 286 - 287: 9.773 distance: 286 - 303: 17.823 distance: 288 - 289: 9.922 distance: 288 - 294: 15.004 distance: 288 - 295: 29.188 distance: 289 - 290: 13.956 distance: 289 - 291: 12.605 distance: 289 - 296: 9.872 distance: 290 - 297: 7.387 distance: 290 - 298: 13.729 distance: 290 - 299: 12.778 distance: 291 - 300: 8.806 distance: 291 - 301: 11.606 distance: 291 - 302: 11.412 distance: 303 - 304: 7.895 distance: 303 - 309: 3.159 distance: 304 - 305: 18.444 distance: 304 - 307: 17.620 distance: 304 - 310: 10.737 distance: 305 - 306: 4.831 distance: 305 - 314: 12.289 distance: 307 - 308: 5.378 distance: 307 - 311: 5.561 distance: 307 - 312: 12.266 distance: 308 - 313: 19.963 distance: 314 - 315: 7.640 distance: 314 - 322: 8.473 distance: 315 - 316: 17.258 distance: 315 - 318: 6.082 distance: 315 - 323: 5.269 distance: 316 - 333: 8.409 distance: 318 - 319: 14.182 distance: 318 - 324: 8.029 distance: 318 - 325: 10.306 distance: 319 - 320: 7.010 distance: 319 - 321: 9.056 distance: 319 - 326: 9.625 distance: 320 - 327: 6.770 distance: 320 - 329: 5.460 distance: 321 - 330: 4.201 distance: 321 - 331: 3.967 distance: 321 - 332: 4.745 distance: 488 - 516: 3.027