Starting phenix.real_space_refine on Sat Jul 4 00:51:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7voo_32052/07_2026/7voo_32052.cif Found real_map, /net/cci-nas-00/data/ceres_data/7voo_32052/07_2026/7voo_32052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7voo_32052/07_2026/7voo_32052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7voo_32052/07_2026/7voo_32052.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7voo_32052/07_2026/7voo_32052.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7voo_32052/07_2026/7voo_32052.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7voo_32052/07_2026/7voo_32052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7voo_32052/07_2026/7voo_32052.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9113 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 6140 2.51 5 N 1609 2.21 5 O 1894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.15s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9686 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1245, 9521 Classifications: {'peptide': 1245} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 61, 'TRANS': 1183} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 4, 'GLU:plan': 9, 'TYR:plan': 2, 'HIS:plan': 2, 'ASN:plan1': 2, 'MEQ:plan-2': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 107 Chain: "B" 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 chiralities: 2 Chain: "C" 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 chiralities: 2 Chain: "D" 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 chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" 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 chiralities: 3 Time building chain proxies: 2.00, per 1000 atoms: 0.21 Number of scatterers: 9686 At special positions: 0 Unit cell: (99.84, 125.84, 124.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1894 8.00 N 1609 7.00 C 6140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 563 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 771 " distance=2.03 Simple disulfide: pdb=" SG CYS A 821 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 847 " - pdb=" SG CYS A 883 " distance=2.03 Simple disulfide: pdb=" SG CYS A 921 " - pdb=" SG CYS A1321 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1127 " 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 ALPHA1-4 " NAG E 2 " - " MAN E 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2101 " - " ASN A 70 " " NAG A2102 " - " ASN A 247 " " NAG A2103 " - " ASN A 396 " " NAG B 1 " - " ASN A 55 " " NAG C 1 " - " ASN A 410 " " NAG D 1 " - " ASN A 869 " " NAG E 1 " - " ASN A 991 " Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 350.5 milliseconds 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2332 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 24 sheets defined 18.8% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 601 through 608 removed outlier: 3.673A pdb=" N LEU A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS A 608 " --> pdb=" O VAL A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 622 removed outlier: 3.869A pdb=" N LEU A 621 " --> pdb=" O SER A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 672 Processing helix chain 'A' and resid 960 through 966 removed outlier: 3.905A pdb=" N LEU A 966 " --> pdb=" O GLN A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 993 removed outlier: 3.671A pdb=" N MET A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 978 " --> pdb=" O GLU A 974 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) Proline residue: A 982 - end of helix removed outlier: 3.674A pdb=" N TYR A 985 " --> pdb=" O ALA A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1016 removed outlier: 3.589A pdb=" N GLY A1006 " --> pdb=" O SER A1002 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A1007 " --> pdb=" O LYS A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1034 Processing helix chain 'A' and resid 1039 through 1053 Processing helix chain 'A' and resid 1059 through 1071 removed outlier: 3.660A pdb=" N ILE A1063 " --> pdb=" O ASP A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1112 removed outlier: 3.838A pdb=" N ILE A1112 " --> pdb=" O ALA A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1138 removed outlier: 3.606A pdb=" N PHE A1126 " --> pdb=" O ARG A1122 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS A1127 " --> pdb=" O ASN A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1157 Processing helix chain 'A' and resid 1159 through 1173 removed outlier: 4.397A pdb=" N GLU A1165 " --> pdb=" O ASP A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1218 removed outlier: 4.190A pdb=" N MET A1208 " --> pdb=" O ALA A1204 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR A1209 " --> pdb=" O GLU A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1241 removed outlier: 4.054A pdb=" N ASN A1233 " --> pdb=" O THR A1229 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE A1234 " --> pdb=" O SER A1230 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TRP A1237 " --> pdb=" O ASN A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1247 Processing helix chain 'A' and resid 1251 through 1269 Processing helix chain 'A' and resid 1293 through 1297 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 3.861A pdb=" N HIS A 85 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 49 " --> pdb=" O HIS A 85 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N LYS A 46 " --> pdb=" O PRO A 36 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 35 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.925A pdb=" N VAL A 60 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA5, first strand: chain 'A' and resid 137 through 138 removed outlier: 3.641A pdb=" N TYR A 138 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 164 " --> pdb=" O GLN A 208 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA A 176 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA7, first strand: chain 'A' and resid 231 through 233 removed outlier: 3.504A pdb=" N GLN A 232 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N CYS A 251 " --> pdb=" O GLN A 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 238 through 239 removed outlier: 3.610A pdb=" N ILE A 239 " --> pdb=" O GLU A 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 287 through 292 removed outlier: 3.514A pdb=" N VAL A 264 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS A 321 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 349 through 354 removed outlier: 4.592A pdb=" N LEU A 350 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL A 372 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE A 352 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ARG A 370 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE A 365 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE A 407 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 369 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 358 through 359 removed outlier: 7.592A pdb=" N PHE A 359 " --> pdb=" O THR A 447 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N TYR A 449 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 458 through 461 removed outlier: 3.732A pdb=" N PHE A 458 " --> pdb=" O ILE A 481 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 474 through 476 Processing sheet with id=AB5, first strand: chain 'A' and resid 493 through 494 Processing sheet with id=AB6, first strand: chain 'A' and resid 504 through 509 removed outlier: 6.767A pdb=" N ILE A 499 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR A 508 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N TYR A 497 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 541 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 552 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 569 through 571 Processing sheet with id=AB8, first strand: chain 'A' and resid 739 through 745 removed outlier: 4.087A pdb=" N ILE A 740 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 792 through 797 removed outlier: 3.626A pdb=" N GLY A 852 " --> pdb=" O ASN A 816 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 801 through 803 removed outlier: 6.057A pdb=" N VAL A 802 " --> pdb=" O GLU A 906 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 847 through 848 removed outlier: 3.822A pdb=" N ILE A 848 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 822 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 872 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 910 through 915 Processing sheet with id=AC4, first strand: chain 'A' and resid 910 through 915 Processing sheet with id=AC5, first strand: chain 'A' and resid 925 through 931 removed outlier: 3.634A pdb=" N GLY A 925 " --> pdb=" O GLY A1318 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR A1312 " --> pdb=" O LEU A 931 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1175 through 1176 325 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3135 1.34 - 1.46: 2226 1.46 - 1.58: 4463 1.58 - 1.70: 0 1.70 - 1.82: 63 Bond restraints: 9887 Sorted by residual: bond pdb=" C1 NAG A2103 " pdb=" O5 NAG A2103 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.68e+00 bond pdb=" CA GLN A 232 " pdb=" CB GLN A 232 " ideal model delta sigma weight residual 1.524 1.568 -0.044 1.62e-02 3.81e+03 7.45e+00 bond pdb=" CA VAL A 260 " pdb=" C VAL A 260 " ideal model delta sigma weight residual 1.524 1.503 0.021 1.05e-02 9.07e+03 4.03e+00 bond pdb=" CA THR A 656 " pdb=" CB THR A 656 " ideal model delta sigma weight residual 1.530 1.557 -0.027 1.58e-02 4.01e+03 2.96e+00 ... (remaining 9882 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.04: 13407 5.04 - 10.08: 35 10.08 - 15.13: 3 15.13 - 20.17: 0 20.17 - 25.21: 2 Bond angle restraints: 13447 Sorted by residual: angle pdb=" C THR A 656 " pdb=" N PRO A 657 " pdb=" CA PRO A 657 " ideal model delta sigma weight residual 119.84 141.14 -21.30 1.25e+00 6.40e-01 2.90e+02 angle pdb=" N PHE A 309 " pdb=" CA PHE A 309 " pdb=" C PHE A 309 " ideal model delta sigma weight residual 109.62 94.94 14.68 1.50e+00 4.44e-01 9.58e+01 angle pdb=" C THR A 656 " pdb=" N PRO A 657 " pdb=" CD PRO A 657 " ideal model delta sigma weight residual 125.00 99.79 25.21 4.10e+00 5.95e-02 3.78e+01 angle pdb=" N GLY A 652 " pdb=" CA GLY A 652 " pdb=" C GLY A 652 " ideal model delta sigma weight residual 113.18 98.93 14.25 2.37e+00 1.78e-01 3.61e+01 angle pdb=" CA PRO A 261 " pdb=" C PRO A 261 " pdb=" N GLY A 262 " ideal model delta sigma weight residual 115.78 109.68 6.10 1.24e+00 6.50e-01 2.42e+01 ... (remaining 13442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 5305 16.01 - 32.02: 439 32.02 - 48.03: 93 48.03 - 64.04: 6 64.04 - 80.05: 12 Dihedral angle restraints: 5855 sinusoidal: 2238 harmonic: 3617 Sorted by residual: dihedral pdb=" CB CYS A 821 " pdb=" SG CYS A 821 " pdb=" SG CYS A 849 " pdb=" CB CYS A 849 " ideal model delta sinusoidal sigma weight residual -86.00 -134.01 48.01 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CA ARG A 684 " pdb=" C ARG A 684 " pdb=" N LYS A 685 " pdb=" CA LYS A 685 " ideal model delta harmonic sigma weight residual 180.00 154.43 25.57 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" C THR A 656 " pdb=" N THR A 656 " pdb=" CA THR A 656 " pdb=" CB THR A 656 " ideal model delta harmonic sigma weight residual -122.00 -133.87 11.87 0 2.50e+00 1.60e-01 2.25e+01 ... (remaining 5852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1509 0.098 - 0.196: 72 0.196 - 0.294: 5 0.294 - 0.392: 2 0.392 - 0.490: 2 Chirality restraints: 1590 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 410 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 55 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CA THR A 656 " pdb=" N THR A 656 " pdb=" C THR A 656 " pdb=" CB THR A 656 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 1587 not shown) Planarity restraints: 1724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 656 " -0.080 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO A 657 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 657 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO A 657 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 308 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.38e+00 pdb=" C VAL A 308 " -0.047 2.00e-02 2.50e+03 pdb=" O VAL A 308 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE A 309 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 578 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO A 579 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 579 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 579 " 0.027 5.00e-02 4.00e+02 ... (remaining 1721 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 98 2.52 - 3.12: 7668 3.12 - 3.71: 15148 3.71 - 4.31: 20366 4.31 - 4.90: 33052 Nonbonded interactions: 76332 Sorted by model distance: nonbonded pdb=" O ASP A 665 " pdb=" OG SER A 668 " model vdw 1.930 3.040 nonbonded pdb=" O GLN A 132 " pdb=" OG1 THR A 133 " model vdw 2.063 3.040 nonbonded pdb=" NH2 ARG A 823 " pdb=" O GLN A 880 " model vdw 2.099 3.120 nonbonded pdb=" O MET A 318 " pdb=" OG SER A 341 " model vdw 2.161 3.040 nonbonded pdb=" O CYS A1079 " pdb=" OG SER A1102 " model vdw 2.172 3.040 ... (remaining 76327 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.740 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9907 Z= 0.208 Angle : 0.936 25.209 13499 Z= 0.502 Chirality : 0.052 0.490 1590 Planarity : 0.005 0.114 1717 Dihedral : 12.618 80.047 3499 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.72 % Favored : 86.87 % Rotamer: Outliers : 0.29 % Allowed : 0.67 % Favored : 99.04 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.23), residues: 1234 helix: 0.10 (0.38), residues: 195 sheet: -1.48 (0.26), residues: 405 loop : -3.06 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 823 TYR 0.026 0.002 TYR A 667 PHE 0.030 0.002 PHE A1057 TRP 0.021 0.002 TRP A1069 HIS 0.003 0.001 HIS A1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.21 ( 9887) covalent geometry : angle 0.91201 / 0.50 (13447) SS BOND : bond 0.00330 / 0.23 ( 8) SS BOND : angle 1.22117 / 0.62 ( 16) hydrogen bonds : bond 0.23762 / 16.07 ( 319) hydrogen bonds : angle 9.11990 / 6.25 ( 879) link_ALPHA1-4 : bond 0.00549 / 0.34 ( 1) link_ALPHA1-4 : angle 1.77842 / 0.89 ( 3) link_BETA1-4 : bond 0.00390 / 0.20 ( 4) link_BETA1-4 : angle 1.69328 / 0.84 ( 12) link_NAG-ASN : bond 0.01294 / 0.87 ( 7) link_NAG-ASN : angle 5.24381 / 3.43 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 500 MET cc_start: 0.8226 (mtp) cc_final: 0.7896 (mtp) REVERT: A 673 MET cc_start: 0.8991 (tpp) cc_final: 0.8662 (tpp) REVERT: A 1323 TYR cc_start: 0.7032 (t80) cc_final: 0.6597 (t80) outliers start: 3 outliers final: 0 residues processed: 128 average time/residue: 0.0725 time to fit residues: 14.2125 Evaluate side-chains 99 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.0010 chunk 51 optimal weight: 0.4980 overall best weight: 3.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN A 368 GLN A 474 GLN ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN A 983 ASN ** A1182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1277 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.115235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.092371 restraints weight = 33956.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.094666 restraints weight = 21265.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.096151 restraints weight = 15596.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.097169 restraints weight = 12738.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.097788 restraints weight = 11122.334| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 9907 Z= 0.206 Angle : 0.827 17.357 13499 Z= 0.416 Chirality : 0.052 0.397 1590 Planarity : 0.006 0.135 1717 Dihedral : 6.575 53.801 1322 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.99 % Favored : 87.68 % Rotamer: Outliers : 2.40 % Allowed : 8.37 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.23), residues: 1234 helix: 0.22 (0.38), residues: 199 sheet: -1.61 (0.25), residues: 432 loop : -3.06 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 787 TYR 0.027 0.002 TYR A 667 PHE 0.016 0.002 PHE A1248 TRP 0.016 0.002 TRP A 739 HIS 0.020 0.002 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 ( 9887) covalent geometry : angle 0.79975 / 0.41 (13447) SS BOND : bond 0.00396 / 0.24 ( 8) SS BOND : angle 0.83071 / 0.48 ( 16) hydrogen bonds : bond 0.04561 / 3.06 ( 319) hydrogen bonds : angle 6.85858 / 4.60 ( 879) link_ALPHA1-4 : bond 0.00243 / 0.15 ( 1) link_ALPHA1-4 : angle 1.42847 / 0.82 ( 3) link_BETA1-4 : bond 0.00499 / 0.30 ( 4) link_BETA1-4 : angle 1.58901 / 0.86 ( 12) link_NAG-ASN : bond 0.01264 / 0.85 ( 7) link_NAG-ASN : angle 5.28387 / 3.38 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 989 TYR cc_start: 0.7984 (t80) cc_final: 0.7760 (t80) REVERT: A 1323 TYR cc_start: 0.6969 (t80) cc_final: 0.6382 (t80) outliers start: 25 outliers final: 16 residues processed: 112 average time/residue: 0.0709 time to fit residues: 12.0231 Evaluate side-chains 108 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1308 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 98 optimal weight: 9.9990 chunk 114 optimal weight: 0.6980 chunk 77 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 73 optimal weight: 40.0000 chunk 49 optimal weight: 8.9990 chunk 30 optimal weight: 0.0670 chunk 58 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 overall best weight: 5.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 279 HIS A 466 HIS A 474 GLN ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN A1277 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.113258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.091641 restraints weight = 34405.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.093090 restraints weight = 23209.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.093429 restraints weight = 17678.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.093950 restraints weight = 17484.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.094245 restraints weight = 14953.871| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 9907 Z= 0.256 Angle : 0.845 16.959 13499 Z= 0.427 Chirality : 0.052 0.406 1590 Planarity : 0.006 0.124 1717 Dihedral : 6.713 51.468 1322 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 13.21 % Favored : 86.47 % Rotamer: Outliers : 3.46 % Allowed : 12.98 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.23), residues: 1234 helix: 0.17 (0.38), residues: 198 sheet: -1.77 (0.24), residues: 445 loop : -3.01 (0.23), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 787 TYR 0.017 0.002 TYR A 667 PHE 0.022 0.002 PHE A 524 TRP 0.014 0.002 TRP A 739 HIS 0.016 0.002 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.26 ( 9887) covalent geometry : angle 0.81909 / 0.42 (13447) SS BOND : bond 0.00468 / 0.28 ( 8) SS BOND : angle 0.84344 / 0.45 ( 16) hydrogen bonds : bond 0.04302 / 2.91 ( 319) hydrogen bonds : angle 6.69097 / 4.44 ( 879) link_ALPHA1-4 : bond 0.00391 / 0.24 ( 1) link_ALPHA1-4 : angle 1.39628 / 0.80 ( 3) link_BETA1-4 : bond 0.00598 / 0.35 ( 4) link_BETA1-4 : angle 1.62312 / 0.90 ( 12) link_NAG-ASN : bond 0.01162 / 0.79 ( 7) link_NAG-ASN : angle 5.24797 / 3.33 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 203 TYR cc_start: 0.6195 (m-10) cc_final: 0.5928 (m-10) outliers start: 36 outliers final: 25 residues processed: 108 average time/residue: 0.0675 time to fit residues: 11.3781 Evaluate side-chains 111 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1314 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 81 optimal weight: 50.0000 chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN A1277 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.112843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.091617 restraints weight = 34192.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.092992 restraints weight = 21425.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.095173 restraints weight = 15732.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.094945 restraints weight = 13629.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.095004 restraints weight = 12267.300| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 9907 Z= 0.224 Angle : 0.814 16.405 13499 Z= 0.407 Chirality : 0.051 0.408 1590 Planarity : 0.006 0.121 1717 Dihedral : 6.656 52.689 1322 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.72 % Favored : 86.95 % Rotamer: Outliers : 4.71 % Allowed : 14.81 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.23), residues: 1234 helix: 0.13 (0.38), residues: 201 sheet: -1.74 (0.25), residues: 439 loop : -3.00 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 360 TYR 0.022 0.002 TYR A 667 PHE 0.025 0.002 PHE A 789 TRP 0.016 0.002 TRP A 739 HIS 0.013 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 ( 9887) covalent geometry : angle 0.78800 / 0.40 (13447) SS BOND : bond 0.00395 / 0.24 ( 8) SS BOND : angle 0.75762 / 0.38 ( 16) hydrogen bonds : bond 0.03802 / 2.54 ( 319) hydrogen bonds : angle 6.42235 / 4.27 ( 879) link_ALPHA1-4 : bond 0.00299 / 0.19 ( 1) link_ALPHA1-4 : angle 1.41518 / 0.81 ( 3) link_BETA1-4 : bond 0.00642 / 0.39 ( 4) link_BETA1-4 : angle 1.58954 / 0.89 ( 12) link_NAG-ASN : bond 0.01178 / 0.79 ( 7) link_NAG-ASN : angle 5.13418 / 3.24 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 94 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 130 PHE cc_start: 0.5921 (OUTLIER) cc_final: 0.5556 (m-10) REVERT: A 203 TYR cc_start: 0.6151 (m-10) cc_final: 0.5929 (m-10) REVERT: A 238 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8188 (pt) REVERT: A 464 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7686 (mtp) REVERT: A 989 TYR cc_start: 0.7671 (t80) cc_final: 0.7211 (t80) REVERT: A 1062 HIS cc_start: 0.6486 (OUTLIER) cc_final: 0.6083 (t-90) REVERT: A 1070 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7370 (mp) REVERT: A 1214 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8789 (mm) outliers start: 49 outliers final: 28 residues processed: 121 average time/residue: 0.0647 time to fit residues: 12.2236 Evaluate side-chains 123 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1062 HIS Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1308 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 83 optimal weight: 40.0000 chunk 68 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 77 optimal weight: 50.0000 chunk 10 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.114471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.092417 restraints weight = 32998.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.094467 restraints weight = 20722.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.096528 restraints weight = 15068.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.096689 restraints weight = 12013.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.096783 restraints weight = 10901.416| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 9907 Z= 0.153 Angle : 0.768 16.262 13499 Z= 0.378 Chirality : 0.050 0.408 1590 Planarity : 0.005 0.117 1717 Dihedral : 6.457 53.073 1322 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.75 % Favored : 87.93 % Rotamer: Outliers : 5.10 % Allowed : 15.48 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.24), residues: 1234 helix: 0.33 (0.38), residues: 201 sheet: -1.61 (0.25), residues: 435 loop : -2.90 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 360 TYR 0.024 0.002 TYR A 667 PHE 0.015 0.002 PHE A 385 TRP 0.018 0.002 TRP A 739 HIS 0.011 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 9887) covalent geometry : angle 0.73994 / 0.37 (13447) SS BOND : bond 0.00268 / 0.17 ( 8) SS BOND : angle 1.33337 / 0.49 ( 16) hydrogen bonds : bond 0.03399 / 2.27 ( 319) hydrogen bonds : angle 6.06340 / 4.02 ( 879) link_ALPHA1-4 : bond 0.00394 / 0.25 ( 1) link_ALPHA1-4 : angle 1.42972 / 0.78 ( 3) link_BETA1-4 : bond 0.00509 / 0.29 ( 4) link_BETA1-4 : angle 1.53378 / 0.84 ( 12) link_NAG-ASN : bond 0.01168 / 0.79 ( 7) link_NAG-ASN : angle 5.03474 / 3.20 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 98 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.5697 (OUTLIER) cc_final: 0.5342 (m-80) REVERT: A 203 TYR cc_start: 0.6053 (m-10) cc_final: 0.5807 (m-10) REVERT: A 253 LEU cc_start: 0.7923 (mp) cc_final: 0.7661 (tt) REVERT: A 989 TYR cc_start: 0.7545 (t80) cc_final: 0.7279 (t80) REVERT: A 1062 HIS cc_start: 0.6113 (OUTLIER) cc_final: 0.5673 (t-90) REVERT: A 1214 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8680 (mm) REVERT: A 1292 VAL cc_start: 0.8071 (OUTLIER) cc_final: 0.7849 (p) outliers start: 53 outliers final: 35 residues processed: 135 average time/residue: 0.0643 time to fit residues: 13.2386 Evaluate side-chains 125 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 86 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 800 TYR Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1062 HIS Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1308 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 80 optimal weight: 40.0000 chunk 117 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 27 optimal weight: 40.0000 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.113397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.091124 restraints weight = 33193.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.093172 restraints weight = 21828.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.094518 restraints weight = 16357.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.095454 restraints weight = 13533.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.095938 restraints weight = 11926.105| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9907 Z= 0.187 Angle : 0.785 15.913 13499 Z= 0.387 Chirality : 0.051 0.416 1590 Planarity : 0.005 0.116 1717 Dihedral : 6.404 53.428 1322 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.16 % Favored : 87.52 % Rotamer: Outliers : 5.58 % Allowed : 16.25 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.24), residues: 1234 helix: 0.33 (0.38), residues: 201 sheet: -1.57 (0.25), residues: 436 loop : -2.85 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 787 TYR 0.023 0.002 TYR A 667 PHE 0.020 0.002 PHE A 385 TRP 0.020 0.002 TRP A 739 HIS 0.010 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 ( 9887) covalent geometry : angle 0.75956 / 0.38 (13447) SS BOND : bond 0.00345 / 0.22 ( 8) SS BOND : angle 1.04228 / 0.49 ( 16) hydrogen bonds : bond 0.03497 / 2.31 ( 319) hydrogen bonds : angle 6.04118 / 4.00 ( 879) link_ALPHA1-4 : bond 0.00369 / 0.23 ( 1) link_ALPHA1-4 : angle 1.33417 / 0.75 ( 3) link_BETA1-4 : bond 0.00441 / 0.26 ( 4) link_BETA1-4 : angle 1.54851 / 0.85 ( 12) link_NAG-ASN : bond 0.01128 / 0.76 ( 7) link_NAG-ASN : angle 4.92886 / 3.12 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 86 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.7972 (tpt) cc_final: 0.7761 (tpt) REVERT: A 130 PHE cc_start: 0.5957 (OUTLIER) cc_final: 0.5206 (m-80) REVERT: A 203 TYR cc_start: 0.6131 (m-10) cc_final: 0.5874 (m-10) REVERT: A 238 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8195 (pt) REVERT: A 495 PHE cc_start: 0.7122 (OUTLIER) cc_final: 0.6690 (m-80) REVERT: A 989 TYR cc_start: 0.7686 (t80) cc_final: 0.7367 (t80) REVERT: A 1214 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8664 (mm) outliers start: 58 outliers final: 38 residues processed: 126 average time/residue: 0.0639 time to fit residues: 12.4289 Evaluate side-chains 125 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 83 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1308 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 113 optimal weight: 0.0470 chunk 20 optimal weight: 20.0000 chunk 88 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN A 381 ASN ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN A1179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.114463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.091814 restraints weight = 32782.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.094049 restraints weight = 20542.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.095553 restraints weight = 15045.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.096489 restraints weight = 12229.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.097149 restraints weight = 10677.371| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 9907 Z= 0.147 Angle : 0.769 15.687 13499 Z= 0.376 Chirality : 0.050 0.412 1590 Planarity : 0.005 0.115 1717 Dihedral : 6.328 53.701 1322 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.51 % Favored : 88.17 % Rotamer: Outliers : 4.71 % Allowed : 17.88 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.24), residues: 1234 helix: 0.41 (0.38), residues: 201 sheet: -1.49 (0.25), residues: 434 loop : -2.83 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 787 TYR 0.025 0.002 TYR A 667 PHE 0.019 0.002 PHE A 130 TRP 0.018 0.002 TRP A 739 HIS 0.008 0.001 HIS A1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 9887) covalent geometry : angle 0.74261 / 0.37 (13447) SS BOND : bond 0.00543 / 0.37 ( 8) SS BOND : angle 1.47639 / 0.66 ( 16) hydrogen bonds : bond 0.03305 / 2.18 ( 319) hydrogen bonds : angle 5.83646 / 3.86 ( 879) link_ALPHA1-4 : bond 0.00347 / 0.22 ( 1) link_ALPHA1-4 : angle 1.36826 / 0.75 ( 3) link_BETA1-4 : bond 0.00470 / 0.27 ( 4) link_BETA1-4 : angle 1.51431 / 0.83 ( 12) link_NAG-ASN : bond 0.01156 / 0.78 ( 7) link_NAG-ASN : angle 4.85836 / 3.09 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 92 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.5794 (OUTLIER) cc_final: 0.5340 (m-80) REVERT: A 203 TYR cc_start: 0.6172 (m-10) cc_final: 0.5887 (m-10) REVERT: A 238 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8232 (pt) REVERT: A 318 MET cc_start: 0.6847 (mpp) cc_final: 0.6287 (mtt) REVERT: A 495 PHE cc_start: 0.7041 (OUTLIER) cc_final: 0.6637 (m-80) REVERT: A 499 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7479 (mp) REVERT: A 989 TYR cc_start: 0.7653 (t80) cc_final: 0.7386 (t80) outliers start: 49 outliers final: 35 residues processed: 123 average time/residue: 0.0627 time to fit residues: 11.9775 Evaluate side-chains 124 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 85 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 800 TYR Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1308 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 29 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 45 optimal weight: 50.0000 chunk 28 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 ASN ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.112445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.089908 restraints weight = 33092.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.091892 restraints weight = 21702.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.093238 restraints weight = 16337.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.093989 restraints weight = 13574.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.094608 restraints weight = 12090.778| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9907 Z= 0.237 Angle : 0.822 15.404 13499 Z= 0.408 Chirality : 0.052 0.421 1590 Planarity : 0.006 0.117 1717 Dihedral : 6.478 52.636 1322 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 13.45 % Favored : 86.22 % Rotamer: Outliers : 4.42 % Allowed : 18.75 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.23), residues: 1234 helix: 0.25 (0.38), residues: 201 sheet: -1.59 (0.25), residues: 437 loop : -2.82 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 360 TYR 0.028 0.002 TYR A 970 PHE 0.025 0.002 PHE A 130 TRP 0.010 0.002 TRP A1040 HIS 0.012 0.002 HIS A1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.24 ( 9887) covalent geometry : angle 0.79764 / 0.40 (13447) SS BOND : bond 0.00465 / 0.29 ( 8) SS BOND : angle 1.53423 / 0.73 ( 16) hydrogen bonds : bond 0.03581 / 2.37 ( 319) hydrogen bonds : angle 6.06033 / 4.02 ( 879) link_ALPHA1-4 : bond 0.00374 / 0.23 ( 1) link_ALPHA1-4 : angle 1.35013 / 0.77 ( 3) link_BETA1-4 : bond 0.00413 / 0.24 ( 4) link_BETA1-4 : angle 1.57670 / 0.87 ( 12) link_NAG-ASN : bond 0.01132 / 0.75 ( 7) link_NAG-ASN : angle 4.82114 / 3.04 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 85 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.6890 (tpp) cc_final: 0.6488 (tpt) REVERT: A 130 PHE cc_start: 0.5766 (OUTLIER) cc_final: 0.5564 (m-80) REVERT: A 203 TYR cc_start: 0.6322 (m-10) cc_final: 0.6011 (m-10) REVERT: A 238 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8184 (pt) REVERT: A 318 MET cc_start: 0.6884 (mpp) cc_final: 0.6347 (mtt) REVERT: A 495 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6778 (m-80) REVERT: A 500 MET cc_start: 0.8477 (mtp) cc_final: 0.7700 (mtm) REVERT: A 554 ASP cc_start: 0.6341 (m-30) cc_final: 0.5742 (m-30) REVERT: A 673 MET cc_start: 0.8371 (tmm) cc_final: 0.7210 (tmm) REVERT: A 989 TYR cc_start: 0.7824 (t80) cc_final: 0.7494 (t80) REVERT: A 1070 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7248 (mp) outliers start: 46 outliers final: 37 residues processed: 117 average time/residue: 0.0695 time to fit residues: 12.5210 Evaluate side-chains 125 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 84 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1308 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 40.0000 chunk 93 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 106 optimal weight: 20.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.113838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.091715 restraints weight = 32981.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.093671 restraints weight = 21776.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.095029 restraints weight = 16464.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.095903 restraints weight = 13674.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.096445 restraints weight = 12051.004| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9907 Z= 0.164 Angle : 0.778 15.171 13499 Z= 0.382 Chirality : 0.051 0.419 1590 Planarity : 0.005 0.116 1717 Dihedral : 6.367 51.539 1322 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.24 % Favored : 87.44 % Rotamer: Outliers : 4.33 % Allowed : 19.23 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.24), residues: 1234 helix: 0.30 (0.38), residues: 208 sheet: -1.52 (0.25), residues: 434 loop : -2.84 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 360 TYR 0.026 0.002 TYR A 970 PHE 0.020 0.002 PHE A 130 TRP 0.013 0.002 TRP A1040 HIS 0.007 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 9887) covalent geometry : angle 0.75390 / 0.38 (13447) SS BOND : bond 0.00469 / 0.31 ( 8) SS BOND : angle 1.14665 / 0.54 ( 16) hydrogen bonds : bond 0.03325 / 2.21 ( 319) hydrogen bonds : angle 5.79899 / 3.85 ( 879) link_ALPHA1-4 : bond 0.00353 / 0.22 ( 1) link_ALPHA1-4 : angle 1.41793 / 0.79 ( 3) link_BETA1-4 : bond 0.00417 / 0.25 ( 4) link_BETA1-4 : angle 1.54580 / 0.85 ( 12) link_NAG-ASN : bond 0.01131 / 0.76 ( 7) link_NAG-ASN : angle 4.75156 / 3.00 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 84 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.5787 (OUTLIER) cc_final: 0.5563 (m-80) REVERT: A 238 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8166 (pt) REVERT: A 318 MET cc_start: 0.6734 (mpp) cc_final: 0.6271 (mtt) REVERT: A 495 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6664 (m-80) REVERT: A 554 ASP cc_start: 0.6106 (m-30) cc_final: 0.5576 (m-30) REVERT: A 988 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7446 (t70) REVERT: A 989 TYR cc_start: 0.7703 (t80) cc_final: 0.7342 (t80) outliers start: 45 outliers final: 34 residues processed: 114 average time/residue: 0.0646 time to fit residues: 11.4801 Evaluate side-chains 121 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 83 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 59 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 30.0000 chunk 116 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.112975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.091964 restraints weight = 32694.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.092956 restraints weight = 21258.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.094307 restraints weight = 16286.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.094363 restraints weight = 14553.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.094460 restraints weight = 13174.332| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 9907 Z= 0.203 Angle : 0.805 14.935 13499 Z= 0.398 Chirality : 0.051 0.422 1590 Planarity : 0.006 0.118 1717 Dihedral : 6.402 50.905 1322 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.32 % Allowed : 13.53 % Favored : 86.14 % Rotamer: Outliers : 4.13 % Allowed : 19.62 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.24), residues: 1234 helix: 0.30 (0.38), residues: 209 sheet: -1.57 (0.25), residues: 440 loop : -2.79 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 360 TYR 0.026 0.002 TYR A 970 PHE 0.024 0.002 PHE A 130 TRP 0.011 0.002 TRP A1040 HIS 0.010 0.002 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 ( 9887) covalent geometry : angle 0.78225 / 0.39 (13447) SS BOND : bond 0.00475 / 0.31 ( 8) SS BOND : angle 1.34006 / 0.64 ( 16) hydrogen bonds : bond 0.03431 / 2.27 ( 319) hydrogen bonds : angle 5.84043 / 3.88 ( 879) link_ALPHA1-4 : bond 0.00348 / 0.22 ( 1) link_ALPHA1-4 : angle 1.33052 / 0.75 ( 3) link_BETA1-4 : bond 0.00431 / 0.25 ( 4) link_BETA1-4 : angle 1.56302 / 0.86 ( 12) link_NAG-ASN : bond 0.01115 / 0.74 ( 7) link_NAG-ASN : angle 4.70332 / 2.95 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 86 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.5835 (OUTLIER) cc_final: 0.5609 (m-80) REVERT: A 238 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8149 (pt) REVERT: A 318 MET cc_start: 0.6783 (mpp) cc_final: 0.6150 (mtm) REVERT: A 495 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.6707 (m-80) REVERT: A 554 ASP cc_start: 0.6340 (m-30) cc_final: 0.5719 (m-30) REVERT: A 988 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7501 (t70) REVERT: A 989 TYR cc_start: 0.7783 (t80) cc_final: 0.7470 (t80) REVERT: A 1070 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7217 (mp) outliers start: 43 outliers final: 36 residues processed: 115 average time/residue: 0.0668 time to fit residues: 12.0083 Evaluate side-chains 125 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 84 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 90 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 23 optimal weight: 0.3980 chunk 47 optimal weight: 0.4980 chunk 119 optimal weight: 8.9990 chunk 104 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.114696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.092832 restraints weight = 32645.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.095071 restraints weight = 22334.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.096028 restraints weight = 15872.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.096267 restraints weight = 14701.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.096404 restraints weight = 13955.650| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 9907 Z= 0.145 Angle : 0.769 14.805 13499 Z= 0.378 Chirality : 0.050 0.417 1590 Planarity : 0.005 0.117 1717 Dihedral : 6.246 50.272 1322 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.99 % Favored : 87.68 % Rotamer: Outliers : 4.13 % Allowed : 19.13 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.24), residues: 1234 helix: 0.46 (0.38), residues: 209 sheet: -1.52 (0.25), residues: 440 loop : -2.75 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 787 TYR 0.026 0.002 TYR A 667 PHE 0.020 0.002 PHE A 130 TRP 0.015 0.002 TRP A1040 HIS 0.010 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 9887) covalent geometry : angle 0.74506 / 0.37 (13447) SS BOND : bond 0.00502 / 0.34 ( 8) SS BOND : angle 1.25632 / 0.58 ( 16) hydrogen bonds : bond 0.03246 / 2.15 ( 319) hydrogen bonds : angle 5.63315 / 3.74 ( 879) link_ALPHA1-4 : bond 0.00294 / 0.18 ( 1) link_ALPHA1-4 : angle 1.40136 / 0.76 ( 3) link_BETA1-4 : bond 0.00464 / 0.27 ( 4) link_BETA1-4 : angle 1.53306 / 0.84 ( 12) link_NAG-ASN : bond 0.01128 / 0.76 ( 7) link_NAG-ASN : angle 4.64828 / 2.93 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1369.21 seconds wall clock time: 24 minutes 33.71 seconds (1473.71 seconds total)