Starting phenix.real_space_refine on Mon Aug 25 07:45:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ovb_17209/08_2025/8ovb_17209.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ovb_17209/08_2025/8ovb_17209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ovb_17209/08_2025/8ovb_17209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ovb_17209/08_2025/8ovb_17209.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ovb_17209/08_2025/8ovb_17209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ovb_17209/08_2025/8ovb_17209.map" } resolution = 3.4 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= 0.002 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 8276 2.51 5 N 2226 2.21 5 O 2495 1.98 5 H 13067 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26116 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 10013 Classifications: {'peptide': 638} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 600} Chain breaks: 1 Chain: "B" Number of atoms: 11899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 11899 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 34, 'TRANS': 716} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 4204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 4204 Classifications: {'peptide': 266} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 258} Chain breaks: 2 Time building chain proxies: 5.16, per 1000 atoms: 0.20 Number of scatterers: 26116 At special positions: 0 Unit cell: (115.648, 136.448, 152.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 2495 8.00 N 2226 7.00 C 8276 6.00 H 13067 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 559 " - pdb=" SG CYS B 816 " distance=2.03 Simple disulfide: pdb=" SG CYS A 627 " - pdb=" SG CYS A 662 " distance=2.03 Simple disulfide: pdb=" SG CYS B 873 " - pdb=" SG CYS B1513 " distance=2.03 Simple disulfide: pdb=" SG CYS B1101 " - pdb=" SG CYS B1158 " distance=2.03 Simple disulfide: pdb=" SG CYS B1358 " - pdb=" SG CYS B1489 " distance=2.03 Simple disulfide: pdb=" SG CYS B1389 " - pdb=" SG CYS B1458 " distance=2.03 Simple disulfide: pdb=" SG CYS B1506 " - pdb=" SG CYS B1511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 200 " distance=2.03 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 181 " 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 Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 943.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3114 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 23 sheets defined 31.5% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 285 through 288 Processing helix chain 'A' and resid 303 through 311 removed outlier: 3.758A pdb=" N VAL A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 480 through 487 removed outlier: 5.620A pdb=" N ALA A 485 " --> pdb=" O ALA A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 526 Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 600 through 606 removed outlier: 3.603A pdb=" N LEU A 605 " --> pdb=" O GLY A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 623 Processing helix chain 'A' and resid 634 through 643 Processing helix chain 'B' and resid 996 through 1003 removed outlier: 4.238A pdb=" N HIS B1002 " --> pdb=" O ARG B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1032 removed outlier: 3.797A pdb=" N MET B1015 " --> pdb=" O GLY B1011 " (cutoff:3.500A) Proline residue: B1020 - end of helix Processing helix chain 'B' and resid 1033 through 1038 Processing helix chain 'B' and resid 1040 through 1059 removed outlier: 4.108A pdb=" N GLY B1044 " --> pdb=" O GLU B1040 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B1058 " --> pdb=" O THR B1054 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE B1059 " --> pdb=" O GLN B1055 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1090 Processing helix chain 'B' and resid 1096 through 1111 removed outlier: 3.614A pdb=" N LEU B1100 " --> pdb=" O ASP B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1126 through 1135 removed outlier: 3.515A pdb=" N ILE B1130 " --> pdb=" O GLN B1127 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY B1132 " --> pdb=" O MET B1129 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN B1135 " --> pdb=" O GLY B1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1159 removed outlier: 4.600A pdb=" N ASP B1156 " --> pdb=" O GLN B1152 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ILE B1157 " --> pdb=" O GLU B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1180 removed outlier: 3.505A pdb=" N ASN B1179 " --> pdb=" O PHE B1175 " (cutoff:3.500A) Processing helix chain 'B' and resid 1181 through 1183 No H-bonds generated for 'chain 'B' and resid 1181 through 1183' Processing helix chain 'B' and resid 1185 through 1198 Processing helix chain 'B' and resid 1204 through 1213 Processing helix chain 'B' and resid 1214 through 1218 removed outlier: 3.886A pdb=" N LYS B1217 " --> pdb=" O ALA B1214 " (cutoff:3.500A) Processing helix chain 'B' and resid 1225 through 1244 removed outlier: 3.646A pdb=" N ASN B1229 " --> pdb=" O LYS B1225 " (cutoff:3.500A) Processing helix chain 'B' and resid 1248 through 1260 removed outlier: 3.904A pdb=" N VAL B1252 " --> pdb=" O PHE B1248 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B1260 " --> pdb=" O LEU B1256 " (cutoff:3.500A) Processing helix chain 'B' and resid 1268 through 1286 Processing helix chain 'B' and resid 1312 through 1316 Processing helix chain 'B' and resid 1414 through 1423 Processing helix chain 'B' and resid 1430 through 1436 Processing helix chain 'B' and resid 1484 through 1488 Processing helix chain 'C' and resid 35 through 55 Processing helix chain 'C' and resid 55 through 86 removed outlier: 3.701A pdb=" N PHE C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA C 68 " --> pdb=" O THR C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 98 Processing helix chain 'C' and resid 99 through 147 removed outlier: 3.819A pdb=" N GLN C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) Proline residue: C 122 - end of helix removed outlier: 3.605A pdb=" N LYS C 133 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 167 Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.719A pdb=" N GLY C 204 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 227 Processing helix chain 'C' and resid 257 through 301 removed outlier: 3.692A pdb=" N GLY C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 88 removed outlier: 8.307A pdb=" N THR A 41 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.143A pdb=" N LEU A 34 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS A 104 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE A 105 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS A 60 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 70 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASP A 61 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL A 68 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 134 Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.528A pdb=" N LYS A 176 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 238 Processing sheet with id=AA6, first strand: chain 'A' and resid 243 through 244 removed outlier: 5.811A pdb=" N TYR A 243 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 324 " --> pdb=" O GLY A 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 243 through 244 removed outlier: 5.811A pdb=" N TYR A 243 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 324 " --> pdb=" O GLY A 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 356 Processing sheet with id=AA9, first strand: chain 'A' and resid 363 through 364 Processing sheet with id=AB1, first strand: chain 'A' and resid 455 through 459 Processing sheet with id=AB2, first strand: chain 'A' and resid 499 through 507 removed outlier: 5.209A pdb=" N LEU A 500 " --> pdb=" O ASN A 496 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASN A 496 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N TYR A 489 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N THR A 536 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 563 through 567 Processing sheet with id=AB4, first strand: chain 'B' and resid 770 through 771 Processing sheet with id=AB5, first strand: chain 'B' and resid 775 through 777 Processing sheet with id=AB6, first strand: chain 'B' and resid 829 through 833 Processing sheet with id=AB7, first strand: chain 'B' and resid 838 through 840 removed outlier: 6.176A pdb=" N VAL B 839 " --> pdb=" O VAL B 932 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 935 through 944 removed outlier: 6.925A pdb=" N VAL B1344 " --> pdb=" O VAL B 942 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL B 944 " --> pdb=" O LEU B1342 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B1342 " --> pdb=" O VAL B 944 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN B 983 " --> pdb=" O THR B1341 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG B1320 " --> pdb=" O LEU B 982 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 957 through 962 Processing sheet with id=AC1, first strand: chain 'B' and resid 1361 through 1363 Processing sheet with id=AC2, first strand: chain 'B' and resid 1361 through 1363 Processing sheet with id=AC3, first strand: chain 'B' and resid 1427 through 1428 Processing sheet with id=AC4, first strand: chain 'B' and resid 1504 through 1507 Processing sheet with id=AC5, first strand: chain 'C' and resid 27 through 29 672 hydrogen bonds defined for protein. 1815 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: 7.81 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13067 1.03 - 1.23: 29 1.23 - 1.42: 5395 1.42 - 1.62: 7796 1.62 - 1.82: 84 Bond restraints: 26371 Sorted by residual: bond pdb=" N ASP B 754 " pdb=" CA ASP B 754 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" N ASP B 754 " pdb=" H ASP B 754 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" CA VAL B 932 " pdb=" CB VAL B 932 " ideal model delta sigma weight residual 1.546 1.535 0.011 8.80e-03 1.29e+04 1.56e+00 bond pdb=" N VAL A 387 " pdb=" CA VAL A 387 " ideal model delta sigma weight residual 1.460 1.467 -0.007 7.50e-03 1.78e+04 9.04e-01 bond pdb=" CA CYS C 181 " pdb=" C CYS C 181 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.16e-02 7.43e+03 7.87e-01 ... (remaining 26366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 47665 2.17 - 4.35: 145 4.35 - 6.52: 9 6.52 - 8.69: 3 8.69 - 10.87: 1 Bond angle restraints: 47823 Sorted by residual: angle pdb=" C ARG A 386 " pdb=" N VAL A 387 " pdb=" CA VAL A 387 " ideal model delta sigma weight residual 122.59 119.80 2.79 7.20e-01 1.93e+00 1.51e+01 angle pdb=" C PHE B1248 " pdb=" N VAL B1249 " pdb=" CA VAL B1249 " ideal model delta sigma weight residual 120.33 123.26 -2.93 8.00e-01 1.56e+00 1.34e+01 angle pdb=" CB MET C 285 " pdb=" CG MET C 285 " pdb=" SD MET C 285 " ideal model delta sigma weight residual 112.70 123.57 -10.87 3.00e+00 1.11e-01 1.31e+01 angle pdb=" N ASN B1137 " pdb=" CA ASN B1137 " pdb=" C ASN B1137 " ideal model delta sigma weight residual 112.72 108.46 4.26 1.28e+00 6.10e-01 1.11e+01 angle pdb=" C VAL B1249 " pdb=" CA VAL B1249 " pdb=" CB VAL B1249 " ideal model delta sigma weight residual 114.00 110.54 3.46 1.31e+00 5.83e-01 6.97e+00 ... (remaining 47818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 11279 17.31 - 34.61: 738 34.61 - 51.92: 254 51.92 - 69.23: 96 69.23 - 86.54: 25 Dihedral angle restraints: 12392 sinusoidal: 6844 harmonic: 5548 Sorted by residual: dihedral pdb=" CB CYS A 627 " pdb=" SG CYS A 627 " pdb=" SG CYS A 662 " pdb=" CB CYS A 662 " ideal model delta sinusoidal sigma weight residual 93.00 170.39 -77.39 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS B 873 " pdb=" SG CYS B 873 " pdb=" SG CYS B1513 " pdb=" CB CYS B1513 " ideal model delta sinusoidal sigma weight residual 93.00 64.01 28.99 1 1.00e+01 1.00e-02 1.20e+01 dihedral pdb=" CA GLN B1465 " pdb=" C GLN B1465 " pdb=" N TYR B1466 " pdb=" CA TYR B1466 " ideal model delta harmonic sigma weight residual 180.00 162.93 17.07 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 12389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1248 0.028 - 0.056: 510 0.056 - 0.084: 108 0.084 - 0.112: 130 0.112 - 0.140: 45 Chirality restraints: 2041 Sorted by residual: chirality pdb=" CA ILE A 348 " pdb=" N ILE A 348 " pdb=" C ILE A 348 " pdb=" CB ILE A 348 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE A 206 " pdb=" N ILE A 206 " pdb=" C ILE A 206 " pdb=" CB ILE A 206 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA ILE A 346 " pdb=" N ILE A 346 " pdb=" C ILE A 346 " pdb=" CB ILE A 346 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 2038 not shown) Planarity restraints: 3895 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B1019 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO B1020 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B1020 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B1020 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 628 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO A 629 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 629 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 629 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 169 " -0.019 5.00e-02 4.00e+02 2.80e-02 1.25e+00 pdb=" N PRO A 170 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " -0.016 5.00e-02 4.00e+02 ... (remaining 3892 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 966 2.17 - 2.78: 52381 2.78 - 3.39: 71439 3.39 - 3.99: 93579 3.99 - 4.60: 146329 Nonbonded interactions: 364694 Sorted by model distance: nonbonded pdb=" O VAL B 971 " pdb=" HG1 THR B 974 " model vdw 1.566 2.450 nonbonded pdb=" OE1 GLN B 856 " pdb=" H GLN B 856 " model vdw 1.595 2.450 nonbonded pdb=" H SER B1452 " pdb=" OD2 ASP B1457 " model vdw 1.610 2.450 nonbonded pdb="HH11 ARG A 102 " pdb=" OE1 GLU B1032 " model vdw 1.613 2.450 nonbonded pdb="HH12 ARG B 848 " pdb=" OD2 ASP B1404 " model vdw 1.624 2.450 ... (remaining 364689 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.160 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.900 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 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 0.039 13313 Z= 0.185 Angle : 0.521 10.867 18040 Z= 0.289 Chirality : 0.041 0.140 2041 Planarity : 0.003 0.032 2324 Dihedral : 13.461 86.536 4994 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 aren not related in a simple way. whole: 1.77 (0.22), residues: 1641 helix: 2.32 (0.26), residues: 412 sheet: 1.08 (0.23), residues: 528 loop : 0.68 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 478 TYR 0.008 0.001 TYR C 209 PHE 0.009 0.001 PHE B1175 TRP 0.008 0.001 TRP B1255 HIS 0.004 0.001 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00379 (13304) covalent geometry : angle 0.51923 (18022) SS BOND : bond 0.00189 ( 9) SS BOND : angle 1.48570 ( 18) hydrogen bonds : bond 0.18813 ( 645) hydrogen bonds : angle 7.54883 ( 1815) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 490 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6503 (mm-30) REVERT: A 82 HIS cc_start: 0.6927 (m-70) cc_final: 0.6604 (m170) REVERT: A 118 GLU cc_start: 0.7735 (pt0) cc_final: 0.7514 (pt0) REVERT: A 177 GLN cc_start: 0.7222 (mt0) cc_final: 0.6986 (mt0) REVERT: A 226 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7065 (mt-10) REVERT: A 237 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6726 (mm-30) REVERT: A 240 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7183 (mt-10) REVERT: A 241 LYS cc_start: 0.8000 (ptpt) cc_final: 0.7654 (mttm) REVERT: A 248 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7156 (mm-30) REVERT: A 254 THR cc_start: 0.7835 (m) cc_final: 0.7634 (p) REVERT: A 258 ARG cc_start: 0.7400 (ptp-170) cc_final: 0.7008 (ptp-110) REVERT: A 264 LYS cc_start: 0.7448 (mtmt) cc_final: 0.7098 (mtmm) REVERT: A 286 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7490 (mm-30) REVERT: A 295 ASP cc_start: 0.7400 (t0) cc_final: 0.6827 (t0) REVERT: A 299 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6932 (mt-10) REVERT: A 325 TYR cc_start: 0.8057 (p90) cc_final: 0.7648 (p90) REVERT: A 399 SER cc_start: 0.7957 (t) cc_final: 0.7341 (p) REVERT: A 451 ASN cc_start: 0.7203 (t0) cc_final: 0.6757 (t0) REVERT: A 489 TYR cc_start: 0.8174 (p90) cc_final: 0.7746 (p90) REVERT: A 502 LYS cc_start: 0.8354 (tttt) cc_final: 0.8026 (tttp) REVERT: A 505 ARG cc_start: 0.7831 (mtt180) cc_final: 0.7266 (mtt180) REVERT: A 509 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6871 (mm-30) REVERT: A 606 ASN cc_start: 0.7568 (t0) cc_final: 0.7335 (t0) REVERT: A 608 LYS cc_start: 0.7468 (mtmm) cc_final: 0.7211 (mtmm) REVERT: A 634 ASP cc_start: 0.6650 (p0) cc_final: 0.6388 (p0) REVERT: A 641 ASP cc_start: 0.7572 (m-30) cc_final: 0.7337 (m-30) REVERT: B 826 MET cc_start: 0.8076 (tpt) cc_final: 0.7837 (tpp) REVERT: B 828 ASP cc_start: 0.7775 (m-30) cc_final: 0.7508 (m-30) REVERT: B 843 GLU cc_start: 0.7505 (tt0) cc_final: 0.6897 (tt0) REVERT: B 859 GLU cc_start: 0.7277 (tt0) cc_final: 0.7073 (tt0) REVERT: B 904 LYS cc_start: 0.7928 (mtpp) cc_final: 0.7548 (mttp) REVERT: B 933 PRO cc_start: 0.8258 (Cg_exo) cc_final: 0.7995 (Cg_endo) REVERT: B 941 THR cc_start: 0.7898 (p) cc_final: 0.7680 (p) REVERT: B 966 ASP cc_start: 0.6348 (t70) cc_final: 0.6120 (t0) REVERT: B 977 GLU cc_start: 0.6741 (tt0) cc_final: 0.6249 (tt0) REVERT: B 1036 LYS cc_start: 0.7498 (mtmt) cc_final: 0.7222 (mtpt) REVERT: B 1186 SER cc_start: 0.6275 (m) cc_final: 0.5585 (p) REVERT: B 1325 LYS cc_start: 0.7019 (mmmm) cc_final: 0.6524 (mmmm) REVERT: B 1348 TYR cc_start: 0.6795 (p90) cc_final: 0.6430 (p90) REVERT: B 1364 LYS cc_start: 0.7453 (tttt) cc_final: 0.6789 (tppp) REVERT: B 1420 GLN cc_start: 0.6846 (tm-30) cc_final: 0.6545 (tm-30) REVERT: B 1423 ASN cc_start: 0.6723 (t0) cc_final: 0.6496 (t0) REVERT: B 1426 ASP cc_start: 0.7538 (m-30) cc_final: 0.7283 (m-30) REVERT: B 1430 SER cc_start: 0.7226 (m) cc_final: 0.6801 (t) REVERT: B 1457 ASP cc_start: 0.5987 (m-30) cc_final: 0.5426 (p0) REVERT: B 1478 LYS cc_start: 0.7265 (ttpt) cc_final: 0.6935 (ttpp) REVERT: B 1487 GLU cc_start: 0.6794 (tt0) cc_final: 0.6248 (tt0) REVERT: B 1513 CYS cc_start: 0.6422 (t) cc_final: 0.6133 (t) REVERT: C 32 LYS cc_start: 0.7596 (pttm) cc_final: 0.7213 (pttm) REVERT: C 33 ASN cc_start: 0.7256 (m-40) cc_final: 0.6790 (m-40) REVERT: C 37 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7690 (mt-10) REVERT: C 44 LYS cc_start: 0.7593 (tptm) cc_final: 0.7290 (mmmm) REVERT: C 89 LYS cc_start: 0.7721 (mtmt) cc_final: 0.7487 (mtmt) REVERT: C 101 SER cc_start: 0.7566 (t) cc_final: 0.7140 (p) REVERT: C 103 ILE cc_start: 0.7770 (mm) cc_final: 0.7514 (mm) REVERT: C 105 LYS cc_start: 0.8116 (mttt) cc_final: 0.7724 (mttt) REVERT: C 123 GLU cc_start: 0.7701 (tp30) cc_final: 0.7336 (tp30) REVERT: C 125 LYS cc_start: 0.7427 (ttmt) cc_final: 0.7203 (ttmt) REVERT: C 126 LYS cc_start: 0.8106 (tttt) cc_final: 0.7352 (tttt) REVERT: C 130 ASP cc_start: 0.6778 (m-30) cc_final: 0.6495 (m-30) REVERT: C 165 ASN cc_start: 0.8352 (m-40) cc_final: 0.7991 (m-40) REVERT: C 229 LYS cc_start: 0.7444 (mtmm) cc_final: 0.7082 (mtmm) REVERT: C 255 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7434 (mt-10) REVERT: C 263 GLU cc_start: 0.7639 (tp30) cc_final: 0.7151 (tp30) REVERT: C 267 LYS cc_start: 0.7766 (mmtp) cc_final: 0.7482 (mmtp) REVERT: C 269 LYS cc_start: 0.7665 (tppt) cc_final: 0.7435 (tppt) REVERT: C 272 GLU cc_start: 0.7656 (tt0) cc_final: 0.7288 (tt0) REVERT: C 276 GLU cc_start: 0.7452 (mt-10) cc_final: 0.6976 (mt-10) outliers start: 0 outliers final: 0 residues processed: 490 average time/residue: 0.3358 time to fit residues: 227.2315 Evaluate side-chains 444 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 183 GLN B1465 GLN C 66 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.110914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.097537 restraints weight = 60541.373| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.16 r_work: 0.3080 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 13313 Z= 0.284 Angle : 0.611 7.553 18040 Z= 0.328 Chirality : 0.047 0.260 2041 Planarity : 0.005 0.066 2324 Dihedral : 4.351 19.420 1782 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.25 % Allowed : 10.77 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 aren not related in a simple way. whole: 1.35 (0.21), residues: 1641 helix: 2.10 (0.26), residues: 421 sheet: 0.85 (0.22), residues: 528 loop : 0.28 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 56 TYR 0.019 0.002 TYR A 147 PHE 0.022 0.002 PHE A 529 TRP 0.012 0.002 TRP A 552 HIS 0.009 0.002 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00655 (13304) covalent geometry : angle 0.60743 (18022) SS BOND : bond 0.00307 ( 9) SS BOND : angle 2.26288 ( 18) hydrogen bonds : bond 0.05180 ( 645) hydrogen bonds : angle 5.69189 ( 1815) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 469 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7992 (m-30) cc_final: 0.7681 (m-30) REVERT: A 65 LYS cc_start: 0.8153 (tppt) cc_final: 0.7801 (tptt) REVERT: A 82 HIS cc_start: 0.7978 (m-70) cc_final: 0.7717 (m170) REVERT: A 154 HIS cc_start: 0.7706 (p90) cc_final: 0.7330 (p90) REVERT: A 225 LYS cc_start: 0.8541 (ttpp) cc_final: 0.8296 (ttpt) REVERT: A 237 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7073 (mm-30) REVERT: A 240 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7728 (pm20) REVERT: A 248 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7283 (mm-30) REVERT: A 254 THR cc_start: 0.8512 (m) cc_final: 0.8203 (p) REVERT: A 258 ARG cc_start: 0.8054 (ptp-170) cc_final: 0.7810 (ptm160) REVERT: A 264 LYS cc_start: 0.8447 (mtmt) cc_final: 0.8021 (mtmm) REVERT: A 295 ASP cc_start: 0.7633 (t0) cc_final: 0.6999 (t0) REVERT: A 299 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7436 (mt-10) REVERT: A 333 HIS cc_start: 0.8155 (m-70) cc_final: 0.7912 (m170) REVERT: A 399 SER cc_start: 0.8481 (t) cc_final: 0.8058 (m) REVERT: A 435 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7350 (mt-10) REVERT: A 451 ASN cc_start: 0.7907 (t0) cc_final: 0.7384 (t0) REVERT: A 488 ARG cc_start: 0.7740 (mtp180) cc_final: 0.7530 (mtp85) REVERT: A 505 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7868 (mtt180) REVERT: A 641 ASP cc_start: 0.7654 (m-30) cc_final: 0.7416 (m-30) REVERT: B 776 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7126 (mm-30) REVERT: B 780 GLU cc_start: 0.7546 (mp0) cc_final: 0.7227 (mp0) REVERT: B 803 GLU cc_start: 0.7959 (tt0) cc_final: 0.7730 (tt0) REVERT: B 822 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7522 (mt-10) REVERT: B 843 GLU cc_start: 0.7800 (tt0) cc_final: 0.7502 (tt0) REVERT: B 894 LEU cc_start: 0.8628 (tp) cc_final: 0.8404 (tt) REVERT: B 904 LYS cc_start: 0.8555 (mtpp) cc_final: 0.8200 (mtmm) REVERT: B 941 THR cc_start: 0.8385 (p) cc_final: 0.8162 (p) REVERT: B 977 GLU cc_start: 0.7565 (tt0) cc_final: 0.7077 (tt0) REVERT: B 982 LEU cc_start: 0.8297 (mm) cc_final: 0.8079 (mp) REVERT: B 1000 LEU cc_start: 0.7844 (mp) cc_final: 0.7631 (mp) REVERT: B 1012 GLU cc_start: 0.7868 (tp30) cc_final: 0.7643 (tp30) REVERT: B 1036 LYS cc_start: 0.8096 (mtmt) cc_final: 0.7880 (mtpt) REVERT: B 1071 LYS cc_start: 0.8333 (mmmt) cc_final: 0.8096 (mmmt) REVERT: B 1160 GLU cc_start: 0.6736 (tm-30) cc_final: 0.6450 (tm-30) REVERT: B 1266 TYR cc_start: 0.6476 (t80) cc_final: 0.6271 (t80) REVERT: B 1298 LEU cc_start: 0.8158 (mt) cc_final: 0.7845 (mt) REVERT: B 1362 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7461 (t0) REVERT: B 1364 LYS cc_start: 0.7960 (tttt) cc_final: 0.7672 (tppp) REVERT: B 1411 PHE cc_start: 0.8514 (m-80) cc_final: 0.8167 (m-80) REVERT: B 1420 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7599 (tm-30) REVERT: B 1423 ASN cc_start: 0.7958 (t0) cc_final: 0.7681 (t0) REVERT: B 1433 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7358 (mm-30) REVERT: B 1478 LYS cc_start: 0.8379 (ttpt) cc_final: 0.8159 (tttt) REVERT: B 1486 GLU cc_start: 0.7446 (pm20) cc_final: 0.7134 (pm20) REVERT: B 1512 ARG cc_start: 0.7996 (mtp-110) cc_final: 0.6570 (mtt90) REVERT: B 1513 CYS cc_start: 0.7378 (t) cc_final: 0.7118 (t) REVERT: C 32 LYS cc_start: 0.7911 (pttm) cc_final: 0.7575 (pttm) REVERT: C 37 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7843 (mt-10) REVERT: C 83 GLU cc_start: 0.7969 (tt0) cc_final: 0.7741 (tt0) REVERT: C 89 LYS cc_start: 0.8034 (mtmt) cc_final: 0.7676 (mtmt) REVERT: C 101 SER cc_start: 0.7857 (t) cc_final: 0.7651 (p) REVERT: C 105 LYS cc_start: 0.8458 (mttt) cc_final: 0.8099 (mttt) REVERT: C 106 VAL cc_start: 0.8617 (t) cc_final: 0.8213 (p) REVERT: C 107 LYS cc_start: 0.8430 (mmtt) cc_final: 0.7885 (mmtt) REVERT: C 123 GLU cc_start: 0.7700 (tp30) cc_final: 0.7452 (tp30) REVERT: C 125 LYS cc_start: 0.8024 (ttmt) cc_final: 0.7745 (ttmt) REVERT: C 126 LYS cc_start: 0.8479 (tttt) cc_final: 0.7772 (tttt) REVERT: C 130 ASP cc_start: 0.7344 (m-30) cc_final: 0.7039 (m-30) REVERT: C 263 GLU cc_start: 0.8023 (tp30) cc_final: 0.7374 (tp30) REVERT: C 267 LYS cc_start: 0.8462 (mmtp) cc_final: 0.8093 (mmtp) REVERT: C 269 LYS cc_start: 0.8292 (tppt) cc_final: 0.7997 (tppt) REVERT: C 272 GLU cc_start: 0.7865 (tt0) cc_final: 0.7582 (tt0) REVERT: C 276 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7327 (mt-10) REVERT: C 288 TYR cc_start: 0.8460 (m-80) cc_final: 0.8022 (m-10) outliers start: 18 outliers final: 12 residues processed: 474 average time/residue: 0.2929 time to fit residues: 191.6682 Evaluate side-chains 461 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 448 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain B residue 1335 GLU Chi-restraints excluded: chain B residue 1362 ASP Chi-restraints excluded: chain B residue 1453 HIS Chi-restraints excluded: chain B residue 1505 LEU Chi-restraints excluded: chain C residue 291 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 72 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN A 569 GLN A 574 GLN A 606 ASN ** B1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1229 ASN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.110004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.096728 restraints weight = 60527.158| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.14 r_work: 0.3086 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 13313 Z= 0.177 Angle : 0.550 9.400 18040 Z= 0.291 Chirality : 0.044 0.275 2041 Planarity : 0.004 0.056 2324 Dihedral : 4.222 19.498 1782 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.60 % Allowed : 12.72 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 aren not related in a simple way. whole: 1.25 (0.21), residues: 1641 helix: 1.97 (0.25), residues: 424 sheet: 0.80 (0.22), residues: 528 loop : 0.25 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 279 TYR 0.020 0.002 TYR B1282 PHE 0.014 0.001 PHE A 529 TRP 0.008 0.001 TRP A 552 HIS 0.005 0.001 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00411 (13304) covalent geometry : angle 0.54261 (18022) SS BOND : bond 0.01056 ( 9) SS BOND : angle 2.93837 ( 18) hydrogen bonds : bond 0.04626 ( 645) hydrogen bonds : angle 5.33793 ( 1815) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 437 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7931 (m-30) cc_final: 0.7599 (m-30) REVERT: A 65 LYS cc_start: 0.8128 (tppt) cc_final: 0.7803 (tptt) REVERT: A 82 HIS cc_start: 0.7969 (m-70) cc_final: 0.7695 (m170) REVERT: A 154 HIS cc_start: 0.7678 (p90) cc_final: 0.7272 (p90) REVERT: A 175 VAL cc_start: 0.8646 (t) cc_final: 0.8354 (m) REVERT: A 225 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8352 (ttpt) REVERT: A 237 GLU cc_start: 0.7550 (mm-30) cc_final: 0.6828 (mm-30) REVERT: A 240 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7523 (pt0) REVERT: A 241 LYS cc_start: 0.8375 (mttm) cc_final: 0.7844 (mmtm) REVERT: A 248 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7267 (mm-30) REVERT: A 254 THR cc_start: 0.8537 (m) cc_final: 0.8212 (p) REVERT: A 258 ARG cc_start: 0.8037 (ptp-170) cc_final: 0.7781 (ptm160) REVERT: A 264 LYS cc_start: 0.8381 (mtmt) cc_final: 0.7964 (mtmm) REVERT: A 277 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6787 (p0) REVERT: A 295 ASP cc_start: 0.7645 (t0) cc_final: 0.7030 (t0) REVERT: A 299 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7382 (mt-10) REVERT: A 399 SER cc_start: 0.8396 (t) cc_final: 0.8000 (m) REVERT: A 435 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7244 (mt-10) REVERT: A 451 ASN cc_start: 0.7889 (t0) cc_final: 0.7410 (t0) REVERT: A 488 ARG cc_start: 0.7695 (mtp180) cc_final: 0.7463 (mtp85) REVERT: A 641 ASP cc_start: 0.7627 (m-30) cc_final: 0.7342 (m-30) REVERT: B 780 GLU cc_start: 0.7545 (mp0) cc_final: 0.7243 (mp0) REVERT: B 803 GLU cc_start: 0.7904 (tt0) cc_final: 0.7676 (tt0) REVERT: B 822 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7441 (mt-10) REVERT: B 843 GLU cc_start: 0.7793 (tt0) cc_final: 0.7496 (tt0) REVERT: B 894 LEU cc_start: 0.8642 (tp) cc_final: 0.8420 (tt) REVERT: B 904 LYS cc_start: 0.8554 (mtpp) cc_final: 0.8208 (mtpp) REVERT: B 977 GLU cc_start: 0.7600 (tt0) cc_final: 0.7072 (tt0) REVERT: B 982 LEU cc_start: 0.8308 (mm) cc_final: 0.8030 (mp) REVERT: B 1012 GLU cc_start: 0.7788 (tp30) cc_final: 0.7451 (tp30) REVERT: B 1036 LYS cc_start: 0.8110 (mtmt) cc_final: 0.7899 (mtpt) REVERT: B 1071 LYS cc_start: 0.8289 (mmmt) cc_final: 0.8083 (mmmt) REVERT: B 1095 ILE cc_start: 0.7856 (mp) cc_final: 0.7619 (mm) REVERT: B 1160 GLU cc_start: 0.6869 (tm-30) cc_final: 0.6599 (tm-30) REVERT: B 1298 LEU cc_start: 0.8107 (mt) cc_final: 0.7816 (mt) REVERT: B 1364 LYS cc_start: 0.7924 (tttt) cc_final: 0.7641 (tppp) REVERT: B 1420 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7584 (tm-30) REVERT: B 1423 ASN cc_start: 0.7984 (t0) cc_final: 0.7707 (t0) REVERT: B 1432 TYR cc_start: 0.8047 (t80) cc_final: 0.7827 (t80) REVERT: B 1433 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7333 (mm-30) REVERT: B 1478 LYS cc_start: 0.8362 (ttpt) cc_final: 0.8135 (tttt) REVERT: B 1512 ARG cc_start: 0.8029 (mtp-110) cc_final: 0.6567 (mtt90) REVERT: B 1513 CYS cc_start: 0.7292 (t) cc_final: 0.7049 (t) REVERT: C 32 LYS cc_start: 0.7949 (pttm) cc_final: 0.7639 (pttm) REVERT: C 37 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7802 (mt-10) REVERT: C 89 LYS cc_start: 0.8051 (mtmt) cc_final: 0.7680 (mtmt) REVERT: C 106 VAL cc_start: 0.8620 (t) cc_final: 0.8211 (p) REVERT: C 107 LYS cc_start: 0.8439 (mmtt) cc_final: 0.7897 (mmtt) REVERT: C 123 GLU cc_start: 0.7745 (tp30) cc_final: 0.7465 (tp30) REVERT: C 125 LYS cc_start: 0.8049 (ttmt) cc_final: 0.7783 (ttmt) REVERT: C 126 LYS cc_start: 0.8468 (tttt) cc_final: 0.7761 (tttt) REVERT: C 130 ASP cc_start: 0.7351 (m-30) cc_final: 0.7032 (m-30) REVERT: C 263 GLU cc_start: 0.8091 (tp30) cc_final: 0.7338 (tp30) REVERT: C 267 LYS cc_start: 0.8482 (mmtp) cc_final: 0.8037 (mmtp) REVERT: C 269 LYS cc_start: 0.8294 (tppt) cc_final: 0.7998 (tppt) REVERT: C 272 GLU cc_start: 0.7861 (tt0) cc_final: 0.7462 (tt0) REVERT: C 276 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7318 (mt-10) REVERT: C 300 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7724 (mm-30) outliers start: 23 outliers final: 14 residues processed: 447 average time/residue: 0.3157 time to fit residues: 192.2833 Evaluate side-chains 440 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 425 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain B residue 1345 VAL Chi-restraints excluded: chain B residue 1358 CYS Chi-restraints excluded: chain B residue 1453 HIS Chi-restraints excluded: chain B residue 1505 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 286 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 73 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 60 optimal weight: 0.0570 chunk 77 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 574 GLN ** B1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1465 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.109940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.095815 restraints weight = 60132.286| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.28 r_work: 0.3046 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 13313 Z= 0.156 Angle : 0.534 9.268 18040 Z= 0.280 Chirality : 0.044 0.287 2041 Planarity : 0.004 0.057 2324 Dihedral : 4.169 18.667 1782 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.81 % Allowed : 13.83 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 aren not related in a simple way. whole: 1.25 (0.21), residues: 1641 helix: 2.00 (0.26), residues: 424 sheet: 0.80 (0.22), residues: 524 loop : 0.21 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 207 TYR 0.023 0.001 TYR B1282 PHE 0.014 0.001 PHE A 529 TRP 0.008 0.001 TRP C 223 HIS 0.007 0.001 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00368 (13304) covalent geometry : angle 0.52636 (18022) SS BOND : bond 0.00711 ( 9) SS BOND : angle 2.90365 ( 18) hydrogen bonds : bond 0.04137 ( 645) hydrogen bonds : angle 5.15117 ( 1815) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 426 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7909 (m-30) cc_final: 0.7556 (m-30) REVERT: A 82 HIS cc_start: 0.7998 (m-70) cc_final: 0.7710 (m170) REVERT: A 175 VAL cc_start: 0.8619 (t) cc_final: 0.8338 (m) REVERT: A 225 LYS cc_start: 0.8593 (ttpp) cc_final: 0.8374 (ttpt) REVERT: A 237 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7031 (mm-30) REVERT: A 240 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7567 (pt0) REVERT: A 248 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7282 (mm-30) REVERT: A 254 THR cc_start: 0.8559 (m) cc_final: 0.8214 (p) REVERT: A 258 ARG cc_start: 0.8010 (ptp-170) cc_final: 0.7772 (ptm160) REVERT: A 264 LYS cc_start: 0.8345 (mtmt) cc_final: 0.7928 (mtmm) REVERT: A 295 ASP cc_start: 0.7761 (t0) cc_final: 0.7138 (t0) REVERT: A 299 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7353 (mt-10) REVERT: A 333 HIS cc_start: 0.8103 (m-70) cc_final: 0.7875 (m170) REVERT: A 399 SER cc_start: 0.8371 (t) cc_final: 0.7968 (m) REVERT: A 421 SER cc_start: 0.8089 (p) cc_final: 0.7843 (p) REVERT: A 435 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7313 (mt-10) REVERT: A 451 ASN cc_start: 0.7944 (t0) cc_final: 0.7463 (t0) REVERT: A 488 ARG cc_start: 0.7680 (mtp180) cc_final: 0.7399 (mtp85) REVERT: A 489 TYR cc_start: 0.8359 (p90) cc_final: 0.8113 (p90) REVERT: A 641 ASP cc_start: 0.7643 (m-30) cc_final: 0.7350 (m-30) REVERT: B 776 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7211 (mp0) REVERT: B 780 GLU cc_start: 0.7563 (mp0) cc_final: 0.7235 (mp0) REVERT: B 803 GLU cc_start: 0.7980 (tt0) cc_final: 0.7767 (tt0) REVERT: B 822 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7459 (mt-10) REVERT: B 843 GLU cc_start: 0.7839 (tt0) cc_final: 0.7532 (tt0) REVERT: B 894 LEU cc_start: 0.8636 (tp) cc_final: 0.8417 (tt) REVERT: B 904 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8228 (mtpp) REVERT: B 977 GLU cc_start: 0.7629 (tt0) cc_final: 0.7112 (tt0) REVERT: B 982 LEU cc_start: 0.8315 (mm) cc_final: 0.8044 (mp) REVERT: B 1032 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7221 (mm-30) REVERT: B 1036 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7915 (mtpt) REVERT: B 1095 ILE cc_start: 0.7973 (mp) cc_final: 0.7742 (mm) REVERT: B 1153 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7571 (mm-30) REVERT: B 1231 GLU cc_start: 0.7510 (tt0) cc_final: 0.7233 (tt0) REVERT: B 1281 GLN cc_start: 0.8025 (tp40) cc_final: 0.7656 (tp40) REVERT: B 1298 LEU cc_start: 0.8098 (mt) cc_final: 0.7819 (mt) REVERT: B 1362 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7430 (t0) REVERT: B 1364 LYS cc_start: 0.7931 (tttt) cc_final: 0.7630 (tppp) REVERT: B 1420 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7556 (tm-30) REVERT: B 1423 ASN cc_start: 0.7929 (t0) cc_final: 0.7663 (t0) REVERT: B 1432 TYR cc_start: 0.7997 (t80) cc_final: 0.7775 (t80) REVERT: B 1433 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7390 (mm-30) REVERT: B 1512 ARG cc_start: 0.8016 (mtp-110) cc_final: 0.6535 (mtt90) REVERT: B 1513 CYS cc_start: 0.7467 (t) cc_final: 0.7239 (t) REVERT: C 32 LYS cc_start: 0.7920 (pttm) cc_final: 0.7611 (pttm) REVERT: C 37 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7865 (mt-10) REVERT: C 83 GLU cc_start: 0.7897 (tt0) cc_final: 0.7689 (tt0) REVERT: C 89 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7776 (mtmt) REVERT: C 106 VAL cc_start: 0.8633 (t) cc_final: 0.8223 (p) REVERT: C 123 GLU cc_start: 0.7781 (tp30) cc_final: 0.7497 (tp30) REVERT: C 125 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7818 (ttmt) REVERT: C 126 LYS cc_start: 0.8458 (tttt) cc_final: 0.7757 (tttt) REVERT: C 130 ASP cc_start: 0.7393 (m-30) cc_final: 0.7065 (m-30) REVERT: C 261 TYR cc_start: 0.8208 (t80) cc_final: 0.7976 (t80) REVERT: C 263 GLU cc_start: 0.8108 (tp30) cc_final: 0.7372 (tp30) REVERT: C 267 LYS cc_start: 0.8486 (mmtp) cc_final: 0.8230 (mmtp) REVERT: C 269 LYS cc_start: 0.8291 (tppt) cc_final: 0.8002 (tppt) REVERT: C 272 GLU cc_start: 0.7893 (tt0) cc_final: 0.7492 (tt0) REVERT: C 276 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7337 (mt-10) REVERT: C 288 TYR cc_start: 0.8541 (m-80) cc_final: 0.8159 (m-10) REVERT: C 300 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7691 (mm-30) outliers start: 26 outliers final: 20 residues processed: 438 average time/residue: 0.3126 time to fit residues: 188.0912 Evaluate side-chains 443 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 422 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain B residue 1345 VAL Chi-restraints excluded: chain B residue 1348 TYR Chi-restraints excluded: chain B residue 1358 CYS Chi-restraints excluded: chain B residue 1362 ASP Chi-restraints excluded: chain B residue 1383 THR Chi-restraints excluded: chain B residue 1426 ASP Chi-restraints excluded: chain B residue 1453 HIS Chi-restraints excluded: chain B residue 1505 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 286 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 86 optimal weight: 0.0060 chunk 109 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.092805 restraints weight = 60890.900| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.34 r_work: 0.3042 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 13313 Z= 0.170 Angle : 0.545 11.155 18040 Z= 0.282 Chirality : 0.044 0.341 2041 Planarity : 0.004 0.050 2324 Dihedral : 4.142 17.849 1782 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.02 % Allowed : 14.38 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 aren not related in a simple way. whole: 1.23 (0.21), residues: 1641 helix: 1.99 (0.25), residues: 424 sheet: 0.79 (0.22), residues: 524 loop : 0.20 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 207 TYR 0.019 0.001 TYR B1282 PHE 0.014 0.001 PHE A 529 TRP 0.008 0.001 TRP A 552 HIS 0.006 0.001 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00405 (13304) covalent geometry : angle 0.53502 (18022) SS BOND : bond 0.00822 ( 9) SS BOND : angle 3.28579 ( 18) hydrogen bonds : bond 0.03987 ( 645) hydrogen bonds : angle 5.04962 ( 1815) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 431 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7921 (m-30) cc_final: 0.7551 (m-30) REVERT: A 82 HIS cc_start: 0.8040 (m-70) cc_final: 0.7750 (m170) REVERT: A 154 HIS cc_start: 0.7696 (p90) cc_final: 0.7328 (p90) REVERT: A 169 ASN cc_start: 0.8143 (t0) cc_final: 0.7892 (m-40) REVERT: A 175 VAL cc_start: 0.8589 (t) cc_final: 0.8319 (m) REVERT: A 237 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7150 (mm-30) REVERT: A 240 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7527 (pt0) REVERT: A 241 LYS cc_start: 0.8470 (mttm) cc_final: 0.8106 (mmtp) REVERT: A 248 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7320 (mm-30) REVERT: A 254 THR cc_start: 0.8543 (m) cc_final: 0.8188 (p) REVERT: A 258 ARG cc_start: 0.8017 (ptp-170) cc_final: 0.7764 (ptm160) REVERT: A 264 LYS cc_start: 0.8310 (mtmt) cc_final: 0.7895 (mtmm) REVERT: A 277 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6803 (p0) REVERT: A 295 ASP cc_start: 0.7806 (t0) cc_final: 0.7194 (t0) REVERT: A 299 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7370 (mt-10) REVERT: A 333 HIS cc_start: 0.8099 (m-70) cc_final: 0.7885 (m170) REVERT: A 342 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7526 (tt0) REVERT: A 399 SER cc_start: 0.8359 (t) cc_final: 0.7941 (m) REVERT: A 421 SER cc_start: 0.8101 (p) cc_final: 0.7865 (p) REVERT: A 451 ASN cc_start: 0.7958 (t0) cc_final: 0.7495 (t0) REVERT: A 488 ARG cc_start: 0.7749 (mtp180) cc_final: 0.7454 (mtp85) REVERT: A 489 TYR cc_start: 0.8353 (p90) cc_final: 0.8032 (p90) REVERT: A 502 LYS cc_start: 0.8423 (tttt) cc_final: 0.8152 (tttm) REVERT: A 505 ARG cc_start: 0.8118 (mtt180) cc_final: 0.7860 (mtt180) REVERT: A 641 ASP cc_start: 0.7692 (m-30) cc_final: 0.7405 (m-30) REVERT: B 776 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7248 (mp0) REVERT: B 780 GLU cc_start: 0.7577 (mp0) cc_final: 0.7242 (mp0) REVERT: B 803 GLU cc_start: 0.7977 (tt0) cc_final: 0.7745 (tt0) REVERT: B 822 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7498 (mt-10) REVERT: B 843 GLU cc_start: 0.7858 (tt0) cc_final: 0.7542 (tt0) REVERT: B 894 LEU cc_start: 0.8611 (tp) cc_final: 0.8408 (tt) REVERT: B 904 LYS cc_start: 0.8620 (mtpp) cc_final: 0.8254 (mtpp) REVERT: B 1032 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7178 (mm-30) REVERT: B 1036 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7941 (mtpt) REVERT: B 1095 ILE cc_start: 0.8049 (mp) cc_final: 0.7830 (mm) REVERT: B 1153 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7559 (mm-30) REVERT: B 1231 GLU cc_start: 0.7500 (tt0) cc_final: 0.7087 (tt0) REVERT: B 1281 GLN cc_start: 0.7961 (tp40) cc_final: 0.7651 (tp40) REVERT: B 1298 LEU cc_start: 0.8061 (mt) cc_final: 0.7783 (mt) REVERT: B 1335 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6938 (mt-10) REVERT: B 1362 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7417 (t0) REVERT: B 1364 LYS cc_start: 0.7949 (tttt) cc_final: 0.7622 (tppp) REVERT: B 1420 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7530 (tm-30) REVERT: B 1423 ASN cc_start: 0.7935 (t0) cc_final: 0.7674 (t0) REVERT: B 1432 TYR cc_start: 0.7982 (t80) cc_final: 0.7762 (t80) REVERT: B 1433 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7380 (mm-30) REVERT: B 1513 CYS cc_start: 0.7500 (t) cc_final: 0.7270 (t) REVERT: C 32 LYS cc_start: 0.7917 (pttm) cc_final: 0.7614 (pttm) REVERT: C 37 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7882 (mt-10) REVERT: C 106 VAL cc_start: 0.8651 (t) cc_final: 0.8251 (p) REVERT: C 123 GLU cc_start: 0.7819 (tp30) cc_final: 0.7543 (tp30) REVERT: C 125 LYS cc_start: 0.8113 (ttmt) cc_final: 0.7845 (ttmt) REVERT: C 126 LYS cc_start: 0.8496 (tttt) cc_final: 0.7766 (tttt) REVERT: C 130 ASP cc_start: 0.7407 (m-30) cc_final: 0.7065 (m-30) REVERT: C 211 TRP cc_start: 0.8511 (m-10) cc_final: 0.8071 (m-10) REVERT: C 263 GLU cc_start: 0.8128 (tp30) cc_final: 0.7350 (tp30) REVERT: C 267 LYS cc_start: 0.8443 (mmtp) cc_final: 0.8155 (mmtp) REVERT: C 269 LYS cc_start: 0.8259 (tppt) cc_final: 0.7975 (tppt) REVERT: C 272 GLU cc_start: 0.7913 (tt0) cc_final: 0.7506 (tt0) REVERT: C 276 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7311 (mt-10) REVERT: C 288 TYR cc_start: 0.8590 (m-80) cc_final: 0.8189 (m-10) REVERT: C 300 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7706 (mm-30) outliers start: 29 outliers final: 20 residues processed: 444 average time/residue: 0.3497 time to fit residues: 214.0072 Evaluate side-chains 446 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 424 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain B residue 1345 VAL Chi-restraints excluded: chain B residue 1348 TYR Chi-restraints excluded: chain B residue 1358 CYS Chi-restraints excluded: chain B residue 1362 ASP Chi-restraints excluded: chain B residue 1383 THR Chi-restraints excluded: chain B residue 1403 LEU Chi-restraints excluded: chain B residue 1426 ASP Chi-restraints excluded: chain B residue 1453 HIS Chi-restraints excluded: chain B residue 1505 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 286 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN B1465 GLN ** C 66 ASN ** 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 = 0.3277 r_free = 0.3277 target = 0.103376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.089247 restraints weight = 61505.811| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.32 r_work: 0.2998 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.138 13313 Z= 0.327 Angle : 0.617 12.069 18040 Z= 0.326 Chirality : 0.047 0.387 2041 Planarity : 0.005 0.054 2324 Dihedral : 4.494 19.530 1782 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.22 % Allowed : 14.32 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 aren not related in a simple way. whole: 0.73 (0.20), residues: 1641 helix: 1.63 (0.25), residues: 421 sheet: 0.51 (0.22), residues: 529 loop : -0.17 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 207 TYR 0.022 0.002 TYR B1180 PHE 0.021 0.002 PHE A 529 TRP 0.016 0.002 TRP C 211 HIS 0.008 0.001 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00764 (13304) covalent geometry : angle 0.60755 (18022) SS BOND : bond 0.01185 ( 9) SS BOND : angle 3.52031 ( 18) hydrogen bonds : bond 0.04628 ( 645) hydrogen bonds : angle 5.15529 ( 1815) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 432 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7982 (m-30) cc_final: 0.7585 (m-30) REVERT: A 82 HIS cc_start: 0.8085 (m-70) cc_final: 0.7884 (m90) REVERT: A 154 HIS cc_start: 0.7703 (p90) cc_final: 0.7305 (p90) REVERT: A 175 VAL cc_start: 0.8602 (t) cc_final: 0.8309 (m) REVERT: A 237 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7270 (mm-30) REVERT: A 240 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7580 (pt0) REVERT: A 248 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7355 (mm-30) REVERT: A 258 ARG cc_start: 0.8036 (ptp-170) cc_final: 0.7794 (ptm160) REVERT: A 295 ASP cc_start: 0.7873 (t0) cc_final: 0.7300 (t0) REVERT: A 299 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7365 (mt-10) REVERT: A 342 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7524 (tt0) REVERT: A 387 VAL cc_start: 0.8464 (OUTLIER) cc_final: 0.8173 (m) REVERT: A 399 SER cc_start: 0.8321 (t) cc_final: 0.7942 (m) REVERT: A 412 ASN cc_start: 0.8078 (m110) cc_final: 0.7870 (m-40) REVERT: A 421 SER cc_start: 0.8104 (p) cc_final: 0.7871 (p) REVERT: A 447 SER cc_start: 0.8437 (t) cc_final: 0.7976 (p) REVERT: A 451 ASN cc_start: 0.8038 (t0) cc_final: 0.7613 (t0) REVERT: A 488 ARG cc_start: 0.7888 (mtp180) cc_final: 0.7644 (mtp85) REVERT: A 502 LYS cc_start: 0.8496 (tttt) cc_final: 0.8279 (tttp) REVERT: A 505 ARG cc_start: 0.8291 (mtt180) cc_final: 0.8087 (mtt180) REVERT: A 641 ASP cc_start: 0.7774 (m-30) cc_final: 0.7522 (m-30) REVERT: B 776 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7327 (mp0) REVERT: B 780 GLU cc_start: 0.7551 (mp0) cc_final: 0.7080 (mp0) REVERT: B 822 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7520 (mt-10) REVERT: B 843 GLU cc_start: 0.7890 (tt0) cc_final: 0.7599 (tt0) REVERT: B 894 LEU cc_start: 0.8605 (tp) cc_final: 0.8384 (tt) REVERT: B 904 LYS cc_start: 0.8644 (mtpp) cc_final: 0.8278 (mtpp) REVERT: B 975 GLU cc_start: 0.7022 (tp30) cc_final: 0.6626 (tp30) REVERT: B 1012 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7195 (mm-30) REVERT: B 1032 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7217 (mm-30) REVERT: B 1153 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7552 (mm-30) REVERT: B 1161 GLN cc_start: 0.7843 (mt0) cc_final: 0.7631 (mt0) REVERT: B 1231 GLU cc_start: 0.7482 (tt0) cc_final: 0.7234 (tt0) REVERT: B 1298 LEU cc_start: 0.8165 (mt) cc_final: 0.7928 (mt) REVERT: B 1323 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7075 (mt-10) REVERT: B 1325 LYS cc_start: 0.7993 (mmmm) cc_final: 0.7590 (mmmm) REVERT: B 1335 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6873 (mt-10) REVERT: B 1364 LYS cc_start: 0.8038 (tttt) cc_final: 0.7697 (tppp) REVERT: B 1420 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7523 (tm-30) REVERT: B 1423 ASN cc_start: 0.7970 (t0) cc_final: 0.7745 (t0) REVERT: B 1433 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7364 (mm-30) REVERT: B 1464 HIS cc_start: 0.7762 (OUTLIER) cc_final: 0.7387 (p-80) REVERT: B 1513 CYS cc_start: 0.7546 (t) cc_final: 0.7301 (t) REVERT: C 32 LYS cc_start: 0.8016 (pttm) cc_final: 0.7691 (pttm) REVERT: C 37 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7944 (mt-10) REVERT: C 74 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7563 (mm-30) REVERT: C 104 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7593 (mm-30) REVERT: C 106 VAL cc_start: 0.8760 (t) cc_final: 0.8384 (p) REVERT: C 107 LYS cc_start: 0.8567 (mmtt) cc_final: 0.7964 (mmtt) REVERT: C 125 LYS cc_start: 0.8173 (ttmt) cc_final: 0.7889 (ttmt) REVERT: C 126 LYS cc_start: 0.8541 (tttt) cc_final: 0.7804 (tttt) REVERT: C 130 ASP cc_start: 0.7462 (m-30) cc_final: 0.7146 (m-30) REVERT: C 211 TRP cc_start: 0.8532 (m-10) cc_final: 0.7786 (m-10) REVERT: C 263 GLU cc_start: 0.8146 (tp30) cc_final: 0.7362 (tp30) REVERT: C 269 LYS cc_start: 0.8287 (tppt) cc_final: 0.7979 (tppt) REVERT: C 272 GLU cc_start: 0.7940 (tt0) cc_final: 0.7520 (tt0) REVERT: C 276 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7341 (mt-10) REVERT: C 288 TYR cc_start: 0.8655 (m-80) cc_final: 0.8201 (m-10) REVERT: C 300 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7773 (mm-30) outliers start: 32 outliers final: 25 residues processed: 445 average time/residue: 0.3174 time to fit residues: 192.8734 Evaluate side-chains 455 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 428 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain B residue 859 GLU Chi-restraints excluded: chain B residue 1110 GLU Chi-restraints excluded: chain B residue 1152 GLN Chi-restraints excluded: chain B residue 1345 VAL Chi-restraints excluded: chain B residue 1348 TYR Chi-restraints excluded: chain B residue 1358 CYS Chi-restraints excluded: chain B residue 1362 ASP Chi-restraints excluded: chain B residue 1366 THR Chi-restraints excluded: chain B residue 1383 THR Chi-restraints excluded: chain B residue 1453 HIS Chi-restraints excluded: chain B residue 1464 HIS Chi-restraints excluded: chain B residue 1505 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 286 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 6 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 71 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1465 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.107763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.093732 restraints weight = 60504.955| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.29 r_work: 0.3026 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 13313 Z= 0.153 Angle : 0.568 20.950 18040 Z= 0.293 Chirality : 0.044 0.359 2041 Planarity : 0.004 0.040 2324 Dihedral : 4.240 19.280 1782 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.22 % Allowed : 14.87 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 aren not related in a simple way. whole: 0.99 (0.21), residues: 1641 helix: 1.79 (0.25), residues: 423 sheet: 0.79 (0.22), residues: 521 loop : -0.08 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 207 TYR 0.017 0.001 TYR B1282 PHE 0.014 0.001 PHE A 529 TRP 0.008 0.001 TRP A 552 HIS 0.005 0.001 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00376 (13304) covalent geometry : angle 0.55381 (18022) SS BOND : bond 0.01187 ( 9) SS BOND : angle 3.97053 ( 18) hydrogen bonds : bond 0.03928 ( 645) hydrogen bonds : angle 4.92816 ( 1815) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 428 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7952 (m-30) cc_final: 0.7563 (m-30) REVERT: A 82 HIS cc_start: 0.8066 (m-70) cc_final: 0.7842 (m90) REVERT: A 154 HIS cc_start: 0.7716 (p90) cc_final: 0.7318 (p90) REVERT: A 175 VAL cc_start: 0.8598 (t) cc_final: 0.8310 (m) REVERT: A 237 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7354 (mm-30) REVERT: A 240 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7581 (pt0) REVERT: A 241 LYS cc_start: 0.8474 (mttm) cc_final: 0.8184 (mmtp) REVERT: A 248 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7337 (mm-30) REVERT: A 258 ARG cc_start: 0.7995 (ptp-170) cc_final: 0.7766 (ptm160) REVERT: A 295 ASP cc_start: 0.7782 (t0) cc_final: 0.7214 (t0) REVERT: A 299 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7343 (mt-10) REVERT: A 342 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7465 (tt0) REVERT: A 387 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8205 (m) REVERT: A 399 SER cc_start: 0.8329 (t) cc_final: 0.7942 (m) REVERT: A 421 SER cc_start: 0.8090 (p) cc_final: 0.7860 (p) REVERT: A 447 SER cc_start: 0.8431 (t) cc_final: 0.7984 (p) REVERT: A 451 ASN cc_start: 0.8037 (t0) cc_final: 0.7614 (t0) REVERT: A 488 ARG cc_start: 0.7806 (mtp180) cc_final: 0.7572 (mtp85) REVERT: A 502 LYS cc_start: 0.8405 (tttt) cc_final: 0.8094 (tttm) REVERT: A 505 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7958 (mtt180) REVERT: A 641 ASP cc_start: 0.7701 (m-30) cc_final: 0.7432 (m-30) REVERT: B 776 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7255 (mp0) REVERT: B 780 GLU cc_start: 0.7551 (mp0) cc_final: 0.7079 (mp0) REVERT: B 822 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7481 (mt-10) REVERT: B 843 GLU cc_start: 0.7869 (tt0) cc_final: 0.7579 (tt0) REVERT: B 894 LEU cc_start: 0.8596 (tp) cc_final: 0.8322 (tt) REVERT: B 904 LYS cc_start: 0.8600 (mtpp) cc_final: 0.8234 (mtpp) REVERT: B 975 GLU cc_start: 0.6944 (tp30) cc_final: 0.6529 (tp30) REVERT: B 977 GLU cc_start: 0.7539 (tt0) cc_final: 0.6886 (tm-30) REVERT: B 982 LEU cc_start: 0.8268 (mm) cc_final: 0.8065 (mt) REVERT: B 1032 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7188 (mm-30) REVERT: B 1095 ILE cc_start: 0.8170 (mp) cc_final: 0.7960 (mm) REVERT: B 1153 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7566 (mm-30) REVERT: B 1161 GLN cc_start: 0.7787 (mt0) cc_final: 0.7583 (mt0) REVERT: B 1231 GLU cc_start: 0.7465 (tt0) cc_final: 0.7234 (tt0) REVERT: B 1325 LYS cc_start: 0.7994 (mmmm) cc_final: 0.7594 (mmmm) REVERT: B 1364 LYS cc_start: 0.7980 (tttt) cc_final: 0.7667 (tppp) REVERT: B 1420 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7537 (tm-30) REVERT: B 1423 ASN cc_start: 0.7939 (t0) cc_final: 0.7719 (t0) REVERT: B 1433 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7306 (mm-30) REVERT: B 1464 HIS cc_start: 0.7704 (OUTLIER) cc_final: 0.7347 (p-80) REVERT: C 32 LYS cc_start: 0.7940 (pttm) cc_final: 0.7615 (pttm) REVERT: C 37 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7917 (mt-10) REVERT: C 74 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7587 (mm-30) REVERT: C 104 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7539 (mm-30) REVERT: C 106 VAL cc_start: 0.8726 (t) cc_final: 0.8330 (p) REVERT: C 107 LYS cc_start: 0.8528 (mmtt) cc_final: 0.7919 (mmtt) REVERT: C 123 GLU cc_start: 0.7766 (tp30) cc_final: 0.7514 (tp30) REVERT: C 125 LYS cc_start: 0.8146 (ttmt) cc_final: 0.7861 (ttmt) REVERT: C 126 LYS cc_start: 0.8509 (tttt) cc_final: 0.7784 (tttt) REVERT: C 130 ASP cc_start: 0.7464 (m-30) cc_final: 0.7147 (m-30) REVERT: C 211 TRP cc_start: 0.8438 (m-10) cc_final: 0.7243 (m-90) REVERT: C 263 GLU cc_start: 0.8111 (tp30) cc_final: 0.7332 (tp30) REVERT: C 269 LYS cc_start: 0.8218 (tppt) cc_final: 0.7880 (tppt) REVERT: C 272 GLU cc_start: 0.7915 (tt0) cc_final: 0.7461 (tt0) REVERT: C 276 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7241 (mt-10) REVERT: C 288 TYR cc_start: 0.8620 (m-80) cc_final: 0.8153 (m-10) REVERT: C 300 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7722 (mm-30) outliers start: 32 outliers final: 21 residues processed: 441 average time/residue: 0.3044 time to fit residues: 183.2101 Evaluate side-chains 446 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 423 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain B residue 859 GLU Chi-restraints excluded: chain B residue 1110 GLU Chi-restraints excluded: chain B residue 1362 ASP Chi-restraints excluded: chain B residue 1383 THR Chi-restraints excluded: chain B residue 1426 ASP Chi-restraints excluded: chain B residue 1453 HIS Chi-restraints excluded: chain B residue 1464 HIS Chi-restraints excluded: chain B residue 1505 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 286 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 78 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN ** B1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1465 GLN ** C 66 ASN ** 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 = 0.3362 r_free = 0.3362 target = 0.108607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.094726 restraints weight = 60259.046| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.30 r_work: 0.3018 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 13313 Z= 0.157 Angle : 0.560 19.884 18040 Z= 0.289 Chirality : 0.044 0.338 2041 Planarity : 0.004 0.039 2324 Dihedral : 4.194 19.585 1782 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.67 % Allowed : 15.84 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 aren not related in a simple way. whole: 1.07 (0.21), residues: 1641 helix: 1.87 (0.25), residues: 423 sheet: 0.83 (0.22), residues: 523 loop : -0.02 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 207 TYR 0.016 0.001 TYR B1432 PHE 0.013 0.001 PHE A 529 TRP 0.013 0.001 TRP C 166 HIS 0.004 0.001 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00375 (13304) covalent geometry : angle 0.55071 (18022) SS BOND : bond 0.01080 ( 9) SS BOND : angle 3.25177 ( 18) hydrogen bonds : bond 0.03790 ( 645) hydrogen bonds : angle 4.84255 ( 1815) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 431 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7963 (m-30) cc_final: 0.7565 (m-30) REVERT: A 82 HIS cc_start: 0.8074 (m-70) cc_final: 0.7830 (m90) REVERT: A 175 VAL cc_start: 0.8624 (t) cc_final: 0.8359 (m) REVERT: A 237 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7389 (mm-30) REVERT: A 240 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7552 (pt0) REVERT: A 241 LYS cc_start: 0.8473 (mttm) cc_final: 0.8199 (mmtp) REVERT: A 248 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7338 (mm-30) REVERT: A 258 ARG cc_start: 0.8000 (ptp-170) cc_final: 0.7772 (ptm160) REVERT: A 277 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6773 (p0) REVERT: A 299 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7355 (mt-10) REVERT: A 333 HIS cc_start: 0.8101 (m-70) cc_final: 0.7887 (m170) REVERT: A 342 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7449 (tt0) REVERT: A 387 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8242 (m) REVERT: A 399 SER cc_start: 0.8336 (t) cc_final: 0.7954 (m) REVERT: A 421 SER cc_start: 0.8088 (p) cc_final: 0.7872 (p) REVERT: A 447 SER cc_start: 0.8419 (t) cc_final: 0.7964 (p) REVERT: A 451 ASN cc_start: 0.8041 (t0) cc_final: 0.7612 (t0) REVERT: A 488 ARG cc_start: 0.7796 (mtp180) cc_final: 0.7564 (mtp85) REVERT: A 502 LYS cc_start: 0.8397 (tttt) cc_final: 0.8170 (tttp) REVERT: A 505 ARG cc_start: 0.8178 (mtt180) cc_final: 0.7920 (mtt180) REVERT: A 641 ASP cc_start: 0.7696 (m-30) cc_final: 0.7436 (m-30) REVERT: B 776 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7249 (mp0) REVERT: B 780 GLU cc_start: 0.7556 (mp0) cc_final: 0.7093 (mp0) REVERT: B 822 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7472 (mt-10) REVERT: B 843 GLU cc_start: 0.7842 (tt0) cc_final: 0.7550 (tt0) REVERT: B 894 LEU cc_start: 0.8595 (tp) cc_final: 0.8325 (tt) REVERT: B 904 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8247 (mtpp) REVERT: B 960 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7494 (mm-30) REVERT: B 977 GLU cc_start: 0.7523 (tt0) cc_final: 0.6948 (tm-30) REVERT: B 1012 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7667 (mm-30) REVERT: B 1095 ILE cc_start: 0.8194 (mp) cc_final: 0.7985 (mm) REVERT: B 1153 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7564 (mm-30) REVERT: B 1161 GLN cc_start: 0.7767 (mt0) cc_final: 0.7518 (mt0) REVERT: B 1231 GLU cc_start: 0.7467 (tt0) cc_final: 0.7147 (tt0) REVERT: B 1364 LYS cc_start: 0.7968 (tttt) cc_final: 0.7640 (tppp) REVERT: B 1383 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8502 (p) REVERT: B 1420 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7534 (tm-30) REVERT: B 1423 ASN cc_start: 0.7938 (t0) cc_final: 0.7725 (t0) REVERT: B 1433 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7291 (mm-30) REVERT: B 1464 HIS cc_start: 0.7694 (OUTLIER) cc_final: 0.7273 (p-80) REVERT: C 32 LYS cc_start: 0.7908 (pttm) cc_final: 0.7607 (pttm) REVERT: C 37 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7915 (mt-10) REVERT: C 74 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7569 (mm-30) REVERT: C 83 GLU cc_start: 0.7865 (tt0) cc_final: 0.7565 (tm-30) REVERT: C 104 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7555 (mm-30) REVERT: C 106 VAL cc_start: 0.8719 (t) cc_final: 0.8321 (p) REVERT: C 107 LYS cc_start: 0.8513 (mmtt) cc_final: 0.7905 (mmtt) REVERT: C 123 GLU cc_start: 0.7745 (tp30) cc_final: 0.7505 (tp30) REVERT: C 125 LYS cc_start: 0.8141 (ttmt) cc_final: 0.7846 (ttmt) REVERT: C 126 LYS cc_start: 0.8505 (tttt) cc_final: 0.7782 (tttt) REVERT: C 130 ASP cc_start: 0.7449 (m-30) cc_final: 0.7094 (m-30) REVERT: C 211 TRP cc_start: 0.8446 (m-10) cc_final: 0.7260 (m-90) REVERT: C 269 LYS cc_start: 0.8224 (tppt) cc_final: 0.7868 (tppt) REVERT: C 272 GLU cc_start: 0.7911 (tt0) cc_final: 0.7447 (tt0) REVERT: C 276 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7228 (mt-10) REVERT: C 277 LYS cc_start: 0.8054 (mttm) cc_final: 0.7408 (mtmm) REVERT: C 288 TYR cc_start: 0.8624 (m-80) cc_final: 0.8136 (m-10) outliers start: 24 outliers final: 18 residues processed: 440 average time/residue: 0.3317 time to fit residues: 198.9210 Evaluate side-chains 448 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 426 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain B residue 1110 GLU Chi-restraints excluded: chain B residue 1362 ASP Chi-restraints excluded: chain B residue 1383 THR Chi-restraints excluded: chain B residue 1426 ASP Chi-restraints excluded: chain B residue 1453 HIS Chi-restraints excluded: chain B residue 1464 HIS Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 286 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1465 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.107576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.093741 restraints weight = 60434.197| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.29 r_work: 0.3010 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.152 13313 Z= 0.242 Angle : 0.581 15.135 18040 Z= 0.303 Chirality : 0.045 0.314 2041 Planarity : 0.004 0.039 2324 Dihedral : 4.332 20.346 1782 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.81 % Allowed : 15.91 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 aren not related in a simple way. whole: 0.88 (0.21), residues: 1641 helix: 1.73 (0.25), residues: 423 sheet: 0.73 (0.22), residues: 519 loop : -0.16 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 207 TYR 0.017 0.002 TYR B1432 PHE 0.018 0.002 PHE A 529 TRP 0.013 0.002 TRP C 166 HIS 0.005 0.001 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00575 (13304) covalent geometry : angle 0.57176 (18022) SS BOND : bond 0.01108 ( 9) SS BOND : angle 3.33787 ( 18) hydrogen bonds : bond 0.04090 ( 645) hydrogen bonds : angle 4.90195 ( 1815) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 434 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7988 (m-30) cc_final: 0.7571 (m-30) REVERT: A 175 VAL cc_start: 0.8621 (t) cc_final: 0.8349 (m) REVERT: A 237 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7410 (mm-30) REVERT: A 240 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7583 (pt0) REVERT: A 241 LYS cc_start: 0.8482 (mttm) cc_final: 0.8216 (mmtp) REVERT: A 248 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7373 (mm-30) REVERT: A 258 ARG cc_start: 0.8036 (ptp-170) cc_final: 0.7801 (ptm160) REVERT: A 295 ASP cc_start: 0.7672 (t0) cc_final: 0.7307 (t0) REVERT: A 299 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7397 (mt-10) REVERT: A 333 HIS cc_start: 0.8122 (m-70) cc_final: 0.7913 (m170) REVERT: A 342 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7482 (tt0) REVERT: A 387 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8245 (m) REVERT: A 412 ASN cc_start: 0.8078 (m110) cc_final: 0.7779 (m-40) REVERT: A 421 SER cc_start: 0.8103 (p) cc_final: 0.7886 (p) REVERT: A 447 SER cc_start: 0.8421 (t) cc_final: 0.7962 (p) REVERT: A 451 ASN cc_start: 0.8028 (t0) cc_final: 0.7582 (t0) REVERT: A 488 ARG cc_start: 0.7822 (mtp180) cc_final: 0.7588 (mtp85) REVERT: A 502 LYS cc_start: 0.8455 (tttt) cc_final: 0.8226 (tttp) REVERT: A 505 ARG cc_start: 0.8234 (mtt180) cc_final: 0.8007 (mtt180) REVERT: A 608 LYS cc_start: 0.8203 (mtmm) cc_final: 0.7998 (mtmm) REVERT: A 641 ASP cc_start: 0.7733 (m-30) cc_final: 0.7488 (m-30) REVERT: B 776 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7298 (mp0) REVERT: B 780 GLU cc_start: 0.7543 (mp0) cc_final: 0.7093 (mp0) REVERT: B 822 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7493 (mt-10) REVERT: B 843 GLU cc_start: 0.7852 (tt0) cc_final: 0.7554 (tt0) REVERT: B 894 LEU cc_start: 0.8608 (tp) cc_final: 0.8331 (tt) REVERT: B 904 LYS cc_start: 0.8629 (mtpp) cc_final: 0.8248 (mtpp) REVERT: B 960 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7560 (mm-30) REVERT: B 977 GLU cc_start: 0.7490 (tt0) cc_final: 0.7005 (tm-30) REVERT: B 1012 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7686 (mm-30) REVERT: B 1095 ILE cc_start: 0.8285 (mp) cc_final: 0.8083 (mm) REVERT: B 1153 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7565 (mm-30) REVERT: B 1161 GLN cc_start: 0.7846 (mt0) cc_final: 0.7597 (mt0) REVERT: B 1231 GLU cc_start: 0.7468 (tt0) cc_final: 0.7143 (tt0) REVERT: B 1323 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7105 (mt-10) REVERT: B 1364 LYS cc_start: 0.8021 (tttt) cc_final: 0.7672 (tppp) REVERT: B 1383 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8533 (p) REVERT: B 1420 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7492 (tm-30) REVERT: B 1423 ASN cc_start: 0.7940 (t0) cc_final: 0.7725 (t0) REVERT: B 1433 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7349 (mm-30) REVERT: B 1464 HIS cc_start: 0.7745 (OUTLIER) cc_final: 0.7270 (p-80) REVERT: C 32 LYS cc_start: 0.7940 (pttm) cc_final: 0.7626 (pttm) REVERT: C 37 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7949 (mt-10) REVERT: C 74 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7560 (mm-30) REVERT: C 83 GLU cc_start: 0.7933 (tt0) cc_final: 0.7626 (tm-30) REVERT: C 104 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7614 (mm-30) REVERT: C 106 VAL cc_start: 0.8763 (t) cc_final: 0.8393 (p) REVERT: C 107 LYS cc_start: 0.8556 (mmtt) cc_final: 0.7945 (mmtt) REVERT: C 123 GLU cc_start: 0.7778 (tp30) cc_final: 0.7557 (tp30) REVERT: C 125 LYS cc_start: 0.8176 (ttmt) cc_final: 0.7883 (ttmt) REVERT: C 126 LYS cc_start: 0.8536 (tttt) cc_final: 0.7820 (tttt) REVERT: C 130 ASP cc_start: 0.7504 (m-30) cc_final: 0.7189 (m-30) REVERT: C 211 TRP cc_start: 0.8538 (m-10) cc_final: 0.7333 (m-90) REVERT: C 269 LYS cc_start: 0.8275 (tppt) cc_final: 0.7925 (tppt) REVERT: C 272 GLU cc_start: 0.7922 (tt0) cc_final: 0.7472 (tt0) REVERT: C 276 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7241 (mt-10) REVERT: C 277 LYS cc_start: 0.8088 (mttm) cc_final: 0.7487 (mtmm) REVERT: C 288 TYR cc_start: 0.8617 (m-80) cc_final: 0.8141 (m-10) outliers start: 26 outliers final: 20 residues processed: 444 average time/residue: 0.3342 time to fit residues: 202.9110 Evaluate side-chains 455 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 432 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain B residue 859 GLU Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1110 GLU Chi-restraints excluded: chain B residue 1348 TYR Chi-restraints excluded: chain B residue 1362 ASP Chi-restraints excluded: chain B residue 1366 THR Chi-restraints excluded: chain B residue 1383 THR Chi-restraints excluded: chain B residue 1453 HIS Chi-restraints excluded: chain B residue 1464 HIS Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 286 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 16 optimal weight: 0.4980 chunk 156 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1465 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.105610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.091407 restraints weight = 60887.630| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.38 r_work: 0.2966 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.147 13313 Z= 0.191 Angle : 0.568 13.714 18040 Z= 0.295 Chirality : 0.044 0.286 2041 Planarity : 0.004 0.040 2324 Dihedral : 4.306 20.648 1782 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.53 % Allowed : 16.68 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 aren not related in a simple way. whole: 0.93 (0.21), residues: 1641 helix: 1.79 (0.25), residues: 423 sheet: 0.72 (0.22), residues: 529 loop : -0.12 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 207 TYR 0.033 0.002 TYR B1282 PHE 0.016 0.001 PHE A 529 TRP 0.024 0.002 TRP B1313 HIS 0.004 0.001 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00457 (13304) covalent geometry : angle 0.55804 (18022) SS BOND : bond 0.00931 ( 9) SS BOND : angle 3.47743 ( 18) hydrogen bonds : bond 0.03890 ( 645) hydrogen bonds : angle 4.81711 ( 1815) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 434 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7544 (tp30) cc_final: 0.7140 (tp30) REVERT: A 52 ASP cc_start: 0.7928 (m-30) cc_final: 0.7504 (m-30) REVERT: A 175 VAL cc_start: 0.8592 (t) cc_final: 0.8341 (m) REVERT: A 237 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7413 (mm-30) REVERT: A 240 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7511 (pt0) REVERT: A 241 LYS cc_start: 0.8496 (mttm) cc_final: 0.8238 (mmtp) REVERT: A 248 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7361 (mm-30) REVERT: A 258 ARG cc_start: 0.7951 (ptp-170) cc_final: 0.7734 (ptm160) REVERT: A 264 LYS cc_start: 0.8182 (mtmt) cc_final: 0.7920 (mtmm) REVERT: A 277 ASP cc_start: 0.7029 (OUTLIER) cc_final: 0.6716 (p0) REVERT: A 295 ASP cc_start: 0.7625 (t0) cc_final: 0.7229 (t0) REVERT: A 299 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7392 (mt-10) REVERT: A 333 HIS cc_start: 0.8125 (m-70) cc_final: 0.7909 (m170) REVERT: A 342 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7503 (tt0) REVERT: A 387 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8227 (m) REVERT: A 399 SER cc_start: 0.8327 (t) cc_final: 0.7926 (m) REVERT: A 421 SER cc_start: 0.8085 (p) cc_final: 0.7878 (p) REVERT: A 447 SER cc_start: 0.8361 (t) cc_final: 0.7896 (p) REVERT: A 451 ASN cc_start: 0.7993 (t0) cc_final: 0.7569 (t0) REVERT: A 488 ARG cc_start: 0.7819 (mtp180) cc_final: 0.7485 (mtp85) REVERT: A 502 LYS cc_start: 0.8379 (tttt) cc_final: 0.8152 (tttp) REVERT: A 505 ARG cc_start: 0.8171 (mtt180) cc_final: 0.7920 (mtt180) REVERT: A 641 ASP cc_start: 0.7758 (m-30) cc_final: 0.7498 (m-30) REVERT: B 758 GLU cc_start: 0.7441 (tm-30) cc_final: 0.7034 (tp30) REVERT: B 776 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7253 (mp0) REVERT: B 780 GLU cc_start: 0.7541 (mp0) cc_final: 0.7069 (mp0) REVERT: B 822 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7495 (mt-10) REVERT: B 843 GLU cc_start: 0.7844 (tt0) cc_final: 0.7520 (tt0) REVERT: B 894 LEU cc_start: 0.8561 (tp) cc_final: 0.8284 (tt) REVERT: B 904 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8216 (mtpp) REVERT: B 977 GLU cc_start: 0.7533 (tt0) cc_final: 0.6887 (tm-30) REVERT: B 1012 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7612 (mm-30) REVERT: B 1095 ILE cc_start: 0.8245 (mp) cc_final: 0.8038 (mm) REVERT: B 1153 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7575 (mm-30) REVERT: B 1161 GLN cc_start: 0.7883 (mt0) cc_final: 0.7600 (mt0) REVERT: B 1231 GLU cc_start: 0.7450 (tt0) cc_final: 0.7106 (tt0) REVERT: B 1364 LYS cc_start: 0.7996 (tttt) cc_final: 0.7625 (tppp) REVERT: B 1383 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8514 (p) REVERT: B 1420 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7453 (tm-30) REVERT: B 1423 ASN cc_start: 0.7893 (t0) cc_final: 0.7671 (t0) REVERT: B 1433 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7304 (mm-30) REVERT: B 1464 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.7231 (p-80) REVERT: C 32 LYS cc_start: 0.7915 (pttm) cc_final: 0.7596 (pttm) REVERT: C 37 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7930 (mt-10) REVERT: C 74 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7568 (mm-30) REVERT: C 83 GLU cc_start: 0.7919 (tt0) cc_final: 0.7613 (tm-30) REVERT: C 104 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7616 (mm-30) REVERT: C 106 VAL cc_start: 0.8724 (t) cc_final: 0.8348 (p) REVERT: C 107 LYS cc_start: 0.8533 (mmtt) cc_final: 0.7923 (mmtt) REVERT: C 123 GLU cc_start: 0.7824 (tp30) cc_final: 0.7574 (tp30) REVERT: C 125 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7841 (ttmt) REVERT: C 126 LYS cc_start: 0.8516 (tttt) cc_final: 0.7787 (tttt) REVERT: C 130 ASP cc_start: 0.7464 (m-30) cc_final: 0.7132 (m-30) REVERT: C 211 TRP cc_start: 0.8507 (m-10) cc_final: 0.7322 (m-90) REVERT: C 253 MET cc_start: 0.7299 (mmm) cc_final: 0.7043 (mmt) REVERT: C 269 LYS cc_start: 0.8238 (tppt) cc_final: 0.7886 (tppt) REVERT: C 272 GLU cc_start: 0.7951 (tt0) cc_final: 0.7468 (tt0) REVERT: C 276 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7219 (mt-10) REVERT: C 277 LYS cc_start: 0.8070 (mttm) cc_final: 0.7445 (mtmm) REVERT: C 288 TYR cc_start: 0.8600 (m-80) cc_final: 0.8125 (m-10) outliers start: 22 outliers final: 16 residues processed: 443 average time/residue: 0.3577 time to fit residues: 216.2695 Evaluate side-chains 448 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 428 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain B residue 859 GLU Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1110 GLU Chi-restraints excluded: chain B residue 1362 ASP Chi-restraints excluded: chain B residue 1383 THR Chi-restraints excluded: chain B residue 1453 HIS Chi-restraints excluded: chain B residue 1464 HIS Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 286 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 0.0010 chunk 91 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 139 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1465 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.109057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.095150 restraints weight = 59883.068| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.27 r_work: 0.3033 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 13313 Z= 0.140 Angle : 0.552 13.909 18040 Z= 0.285 Chirality : 0.044 0.265 2041 Planarity : 0.004 0.039 2324 Dihedral : 4.241 21.822 1782 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.32 % Allowed : 17.37 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 aren not related in a simple way. whole: 1.03 (0.21), residues: 1641 helix: 1.90 (0.26), residues: 423 sheet: 0.77 (0.22), residues: 529 loop : -0.08 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1512 TYR 0.026 0.001 TYR B1282 PHE 0.018 0.001 PHE B1246 TRP 0.035 0.002 TRP B1313 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00337 (13304) covalent geometry : angle 0.54374 (18022) SS BOND : bond 0.00786 ( 9) SS BOND : angle 3.02263 ( 18) hydrogen bonds : bond 0.03645 ( 645) hydrogen bonds : angle 4.73398 ( 1815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6860.33 seconds wall clock time: 117 minutes 2.17 seconds (7022.17 seconds total)