Starting phenix.real_space_refine on Sun May 25 02:54:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ovb_17209/05_2025/8ovb_17209.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ovb_17209/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ovb_17209/05_2025/8ovb_17209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ovb_17209/05_2025/8ovb_17209.map" model { file = "/net/cci-nas-00/data/ceres_data/8ovb_17209/05_2025/8ovb_17209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ovb_17209/05_2025/8ovb_17209.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.58, per 1000 atoms: 0.44 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: 6.65 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 2.39 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: 10.63 Time building geometry restraints manager: 7.95 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: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.420 Extract box with map and model: 0.980 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 53.090 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.010 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.008 0.001 TRP B1255 HIS 0.004 0.001 HIS C 282 PHE 0.009 0.001 PHE B1175 TYR 0.008 0.001 TYR C 209 ARG 0.003 0.000 ARG A 478 Details of bonding type rmsd hydrogen bonds : bond 0.18813 ( 645) hydrogen bonds : angle 7.54883 ( 1815) SS BOND : bond 0.00189 ( 9) SS BOND : angle 1.48570 ( 18) covalent geometry : bond 0.00379 (13304) covalent geometry : angle 0.51923 (18022) *********************** 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 : 1.788 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: 0.6502 (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: 0.6985 (mt0) REVERT: A 226 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7066 (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: 0.7099 (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 633 LYS cc_start: 0.7554 (pttp) cc_final: 0.7354 (pttp) REVERT: A 634 ASP cc_start: 0.6650 (p0) cc_final: 0.6387 (p0) REVERT: A 641 ASP cc_start: 0.7572 (m-30) cc_final: 0.7336 (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: 0.7221 (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: 0.6523 (mmmm) REVERT: B 1348 TYR cc_start: 0.6795 (p90) cc_final: 0.6431 (p90) REVERT: B 1364 LYS cc_start: 0.7453 (tttt) cc_final: 0.6790 (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: 0.7282 (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: 0.5425 (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: 0.6247 (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: 0.7214 (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: 0.7513 (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: 0.7204 (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: 0.7990 (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: 0.7433 (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: 0.7436 (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: 0.6470 time to fit residues: 437.8766 Evaluate side-chains 445 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.110882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.097467 restraints weight = 60463.144| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.17 r_work: 0.3089 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 13313 Z= 0.258 Angle : 0.602 8.539 18040 Z= 0.324 Chirality : 0.047 0.229 2041 Planarity : 0.005 0.060 2324 Dihedral : 4.270 18.692 1782 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.25 % Allowed : 10.84 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.21), residues: 1641 helix: 2.18 (0.26), residues: 421 sheet: 0.86 (0.22), residues: 528 loop : 0.32 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 552 HIS 0.009 0.001 HIS C 282 PHE 0.020 0.002 PHE A 529 TYR 0.017 0.002 TYR B1282 ARG 0.011 0.001 ARG C 56 Details of bonding type rmsd hydrogen bonds : bond 0.04922 ( 645) hydrogen bonds : angle 5.70535 ( 1815) SS BOND : bond 0.00448 ( 9) SS BOND : angle 2.37668 ( 18) covalent geometry : bond 0.00602 (13304) covalent geometry : angle 0.59767 (18022) *********************** 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 496 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 478 time to evaluate : 2.050 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: 0.7957 (m-30) cc_final: 0.7651 (m-30) REVERT: A 72 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7280 (mm-30) REVERT: A 82 HIS cc_start: 0.7956 (m-70) cc_final: 0.7703 (m170) REVERT: A 154 HIS cc_start: 0.7689 (p90) cc_final: 0.7308 (p90) REVERT: A 169 ASN cc_start: 0.8091 (t0) cc_final: 0.7883 (m-40) REVERT: A 225 LYS cc_start: 0.8543 (ttpp) cc_final: 0.8287 (ttpt) REVERT: A 237 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7071 (mm-30) REVERT: A 240 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7718 (pm20) REVERT: A 241 LYS cc_start: 0.8510 (ptpt) cc_final: 0.8297 (mttm) REVERT: A 246 TYR cc_start: 0.8286 (m-80) cc_final: 0.8072 (m-80) REVERT: A 248 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7301 (mm-30) REVERT: A 254 THR cc_start: 0.8512 (m) cc_final: 0.8196 (p) REVERT: A 258 ARG cc_start: 0.8046 (ptp-170) cc_final: 0.7836 (ptp-110) REVERT: A 264 LYS cc_start: 0.8430 (mtmt) cc_final: 0.7986 (mtmm) REVERT: A 295 ASP cc_start: 0.7616 (t0) cc_final: 0.6980 (t0) REVERT: A 299 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7423 (mt-10) REVERT: A 399 SER cc_start: 0.8463 (t) cc_final: 0.8045 (m) REVERT: A 435 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7252 (mt-10) REVERT: A 451 ASN cc_start: 0.7928 (t0) cc_final: 0.7396 (t0) REVERT: A 488 ARG cc_start: 0.7684 (mtp180) cc_final: 0.7464 (mtp85) REVERT: A 505 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7875 (mtt180) REVERT: A 509 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7462 (mm-30) REVERT: A 633 LYS cc_start: 0.8484 (pttp) cc_final: 0.8218 (pttp) REVERT: A 641 ASP cc_start: 0.7666 (m-30) cc_final: 0.7424 (m-30) REVERT: B 776 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7127 (mm-30) REVERT: B 780 GLU cc_start: 0.7549 (mp0) cc_final: 0.7228 (mp0) REVERT: B 803 GLU cc_start: 0.7954 (tt0) cc_final: 0.7721 (tt0) REVERT: B 822 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7445 (mt-10) REVERT: B 843 GLU cc_start: 0.7791 (tt0) cc_final: 0.7492 (tt0) REVERT: B 894 LEU cc_start: 0.8627 (tp) cc_final: 0.8393 (tt) REVERT: B 904 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8209 (mtmm) REVERT: B 941 THR cc_start: 0.8345 (p) cc_final: 0.8119 (p) REVERT: B 977 GLU cc_start: 0.7550 (tt0) cc_final: 0.7047 (tt0) REVERT: B 982 LEU cc_start: 0.8273 (mm) cc_final: 0.8063 (mp) REVERT: B 990 MET cc_start: 0.5797 (tmm) cc_final: 0.5562 (tmm) REVERT: B 1000 LEU cc_start: 0.7821 (mp) cc_final: 0.7595 (mp) REVERT: B 1012 GLU cc_start: 0.7861 (tp30) cc_final: 0.7625 (tp30) REVERT: B 1036 LYS cc_start: 0.8105 (mtmt) cc_final: 0.7883 (mtpt) REVERT: B 1071 LYS cc_start: 0.8328 (mmmt) cc_final: 0.8085 (mmmt) REVERT: B 1129 MET cc_start: 0.7918 (tpp) cc_final: 0.7690 (tpp) REVERT: B 1160 GLU cc_start: 0.6692 (tm-30) cc_final: 0.6413 (tm-30) REVERT: B 1186 SER cc_start: 0.8203 (m) cc_final: 0.7882 (t) REVERT: B 1298 LEU cc_start: 0.8106 (mt) cc_final: 0.7772 (mt) REVERT: B 1362 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7444 (t0) REVERT: B 1364 LYS cc_start: 0.7939 (tttt) cc_final: 0.7646 (tppp) REVERT: B 1411 PHE cc_start: 0.8477 (m-80) cc_final: 0.8171 (m-80) REVERT: B 1420 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7596 (tm-30) REVERT: B 1423 ASN cc_start: 0.7953 (t0) cc_final: 0.7660 (t0) REVERT: B 1433 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7375 (mm-30) REVERT: B 1478 LYS cc_start: 0.8379 (ttpt) cc_final: 0.8151 (tttt) REVERT: B 1486 GLU cc_start: 0.7422 (pm20) cc_final: 0.7066 (pm20) REVERT: B 1512 ARG cc_start: 0.7955 (mtp-110) cc_final: 0.6525 (mtt90) REVERT: B 1513 CYS cc_start: 0.7343 (t) cc_final: 0.7076 (t) REVERT: C 32 LYS cc_start: 0.7888 (pttm) cc_final: 0.7550 (pttm) REVERT: C 37 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7838 (mt-10) REVERT: C 83 GLU cc_start: 0.7940 (tt0) cc_final: 0.7706 (tt0) REVERT: C 89 LYS cc_start: 0.8020 (mtmt) cc_final: 0.7652 (mtmt) REVERT: C 105 LYS cc_start: 0.8381 (mttt) cc_final: 0.8034 (mttt) REVERT: C 106 VAL cc_start: 0.8593 (t) cc_final: 0.8190 (p) REVERT: C 123 GLU cc_start: 0.7670 (tp30) cc_final: 0.7417 (tp30) REVERT: C 125 LYS cc_start: 0.8007 (ttmt) cc_final: 0.7733 (ttmt) REVERT: C 126 LYS cc_start: 0.8461 (tttt) cc_final: 0.7742 (tttt) REVERT: C 130 ASP cc_start: 0.7318 (m-30) cc_final: 0.7018 (m-30) REVERT: C 263 GLU cc_start: 0.8007 (tp30) cc_final: 0.7372 (tp30) REVERT: C 267 LYS cc_start: 0.8460 (mmtp) cc_final: 0.8087 (mmtp) REVERT: C 269 LYS cc_start: 0.8283 (tppt) cc_final: 0.7986 (tppt) REVERT: C 272 GLU cc_start: 0.7854 (tt0) cc_final: 0.7529 (tt0) REVERT: C 276 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7310 (mt-10) REVERT: C 288 TYR cc_start: 0.8447 (m-80) cc_final: 0.8019 (m-10) outliers start: 18 outliers final: 11 residues processed: 482 average time/residue: 0.6949 time to fit residues: 467.4768 Evaluate side-chains 463 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 451 time to evaluate : 2.108 ------------------------------------------------------------------------------- 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 67 LEU 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 A residue 614 SER 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 133 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 163 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.110856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.097613 restraints weight = 60185.937| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.15 r_work: 0.3082 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 13313 Z= 0.165 Angle : 0.540 9.792 18040 Z= 0.285 Chirality : 0.044 0.275 2041 Planarity : 0.004 0.063 2324 Dihedral : 4.180 19.686 1782 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.46 % Allowed : 12.93 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.21), residues: 1641 helix: 2.01 (0.25), residues: 424 sheet: 0.72 (0.22), residues: 538 loop : 0.32 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 223 HIS 0.006 0.001 HIS C 282 PHE 0.013 0.001 PHE A 529 TYR 0.026 0.001 TYR B1432 ARG 0.005 0.000 ARG C 279 Details of bonding type rmsd hydrogen bonds : bond 0.04581 ( 645) hydrogen bonds : angle 5.36309 ( 1815) SS BOND : bond 0.00534 ( 9) SS BOND : angle 3.19135 ( 18) covalent geometry : bond 0.00377 (13304) covalent geometry : angle 0.53100 (18022) *********************** 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 457 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 436 time to evaluate : 1.988 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: 0.7941 (m-30) cc_final: 0.7607 (m-30) REVERT: A 65 LYS cc_start: 0.8107 (tppt) cc_final: 0.7804 (tptt) REVERT: A 82 HIS cc_start: 0.7962 (m-70) cc_final: 0.7698 (m170) REVERT: A 175 VAL cc_start: 0.8635 (t) cc_final: 0.8355 (m) REVERT: A 225 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8360 (ttpt) REVERT: A 241 LYS cc_start: 0.8542 (ptpt) cc_final: 0.8320 (mttm) REVERT: A 248 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7269 (mm-30) REVERT: A 254 THR cc_start: 0.8574 (m) cc_final: 0.8248 (p) REVERT: A 258 ARG cc_start: 0.8050 (ptp-170) cc_final: 0.7817 (ptm160) REVERT: A 264 LYS cc_start: 0.8400 (mtmt) cc_final: 0.7963 (mtmm) REVERT: A 295 ASP cc_start: 0.7633 (t0) cc_final: 0.7011 (t0) REVERT: A 299 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7367 (mt-10) REVERT: A 399 SER cc_start: 0.8387 (t) cc_final: 0.7994 (m) REVERT: A 435 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7248 (mt-10) REVERT: A 451 ASN cc_start: 0.7934 (t0) cc_final: 0.7443 (t0) REVERT: A 488 ARG cc_start: 0.7680 (mtp180) cc_final: 0.7400 (mtp85) REVERT: A 505 ARG cc_start: 0.8080 (mtt180) cc_final: 0.7866 (mtt180) REVERT: A 633 LYS cc_start: 0.8470 (pttp) cc_final: 0.8213 (pttp) REVERT: A 641 ASP cc_start: 0.7631 (m-30) cc_final: 0.7345 (m-30) REVERT: B 758 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6997 (tm-30) REVERT: B 780 GLU cc_start: 0.7517 (mp0) cc_final: 0.7235 (mp0) REVERT: B 803 GLU cc_start: 0.7931 (tt0) cc_final: 0.7727 (tt0) REVERT: B 822 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7398 (mt-10) REVERT: B 843 GLU cc_start: 0.7783 (tt0) cc_final: 0.7476 (tt0) REVERT: B 865 GLU cc_start: 0.7897 (pt0) cc_final: 0.7622 (pt0) REVERT: B 894 LEU cc_start: 0.8656 (tp) cc_final: 0.8427 (tt) REVERT: B 904 LYS cc_start: 0.8536 (mtpp) cc_final: 0.8197 (mtpp) REVERT: B 977 GLU cc_start: 0.7614 (tt0) cc_final: 0.7099 (tt0) REVERT: B 982 LEU cc_start: 0.8287 (mm) cc_final: 0.8019 (mp) REVERT: B 1012 GLU cc_start: 0.7867 (tp30) cc_final: 0.7584 (mm-30) REVERT: B 1036 LYS cc_start: 0.8112 (mtmt) cc_final: 0.7895 (mtpt) REVERT: B 1071 LYS cc_start: 0.8278 (mmmt) cc_final: 0.8057 (mmmt) REVERT: B 1096 ASP cc_start: 0.7865 (m-30) cc_final: 0.7331 (p0) REVERT: B 1129 MET cc_start: 0.7931 (tpp) cc_final: 0.7700 (tpp) REVERT: B 1153 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7433 (mm-30) REVERT: B 1231 GLU cc_start: 0.7419 (tt0) cc_final: 0.7162 (tt0) REVERT: B 1298 LEU cc_start: 0.8088 (mt) cc_final: 0.7776 (mt) REVERT: B 1364 LYS cc_start: 0.7914 (tttt) cc_final: 0.7650 (tppp) REVERT: B 1420 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7608 (tm-30) REVERT: B 1423 ASN cc_start: 0.8002 (t0) cc_final: 0.7733 (t0) REVERT: B 1433 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7332 (mm-30) REVERT: B 1478 LYS cc_start: 0.8371 (ttpt) cc_final: 0.8144 (tttt) REVERT: B 1512 ARG cc_start: 0.8015 (mtp-110) cc_final: 0.6541 (mtt90) REVERT: B 1513 CYS cc_start: 0.7308 (t) cc_final: 0.7066 (t) REVERT: C 32 LYS cc_start: 0.7936 (pttm) cc_final: 0.7633 (pttm) REVERT: C 37 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7798 (mt-10) REVERT: C 89 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7628 (mtmt) REVERT: C 106 VAL cc_start: 0.8593 (t) cc_final: 0.8176 (p) REVERT: C 107 LYS cc_start: 0.8403 (mmtt) cc_final: 0.7853 (mmtt) REVERT: C 123 GLU cc_start: 0.7706 (tp30) cc_final: 0.7444 (tp30) REVERT: C 125 LYS cc_start: 0.8029 (ttmt) cc_final: 0.7738 (ttmt) REVERT: C 126 LYS cc_start: 0.8457 (tttt) cc_final: 0.7756 (tttt) REVERT: C 130 ASP cc_start: 0.7320 (m-30) cc_final: 0.7016 (m-30) REVERT: C 263 GLU cc_start: 0.8081 (tp30) cc_final: 0.7331 (tp30) REVERT: C 267 LYS cc_start: 0.8505 (mmtp) cc_final: 0.8071 (mmtp) REVERT: C 269 LYS cc_start: 0.8314 (tppt) cc_final: 0.8019 (tppt) REVERT: C 272 GLU cc_start: 0.7859 (tt0) cc_final: 0.7549 (tt0) REVERT: C 276 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7312 (mt-10) outliers start: 21 outliers final: 13 residues processed: 442 average time/residue: 0.6953 time to fit residues: 424.0545 Evaluate side-chains 443 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 430 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 186 LEU 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 1335 GLU Chi-restraints excluded: chain B residue 1345 VAL 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 121 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 86 optimal weight: 0.0170 chunk 69 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 GLN B 774 ASN 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 = 0.3345 r_free = 0.3345 target = 0.107577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.093331 restraints weight = 61208.247| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.32 r_work: 0.2995 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 13313 Z= 0.231 Angle : 0.562 10.755 18040 Z= 0.296 Chirality : 0.045 0.293 2041 Planarity : 0.004 0.054 2324 Dihedral : 4.262 18.645 1782 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.60 % Allowed : 13.83 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.21), residues: 1641 helix: 1.86 (0.25), residues: 423 sheet: 0.69 (0.22), residues: 528 loop : 0.12 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 552 HIS 0.007 0.001 HIS C 282 PHE 0.017 0.002 PHE A 529 TYR 0.022 0.002 TYR B1282 ARG 0.008 0.001 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 645) hydrogen bonds : angle 5.22052 ( 1815) SS BOND : bond 0.00968 ( 9) SS BOND : angle 3.43303 ( 18) covalent geometry : bond 0.00539 (13304) covalent geometry : angle 0.55136 (18022) *********************** 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 447 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 424 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7927 (m-30) cc_final: 0.7559 (m-30) REVERT: A 82 HIS cc_start: 0.8010 (m-70) cc_final: 0.7686 (m170) REVERT: A 154 HIS cc_start: 0.7693 (p90) cc_final: 0.7325 (p90) REVERT: A 175 VAL cc_start: 0.8614 (t) cc_final: 0.8321 (m) REVERT: A 225 LYS cc_start: 0.8577 (ttpp) cc_final: 0.8350 (ttpt) REVERT: A 241 LYS cc_start: 0.8578 (ptpt) cc_final: 0.8301 (mttm) REVERT: A 248 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7310 (mm-30) REVERT: A 254 THR cc_start: 0.8534 (m) cc_final: 0.8184 (p) REVERT: A 258 ARG cc_start: 0.8026 (ptp-170) cc_final: 0.7774 (ptm160) REVERT: A 264 LYS cc_start: 0.8355 (mtmt) cc_final: 0.7930 (mtmm) REVERT: A 295 ASP cc_start: 0.7803 (t0) cc_final: 0.7176 (t0) REVERT: A 299 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7358 (mt-10) REVERT: A 399 SER cc_start: 0.8391 (t) cc_final: 0.7962 (m) REVERT: A 435 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7278 (mt-10) REVERT: A 451 ASN cc_start: 0.7932 (t0) cc_final: 0.7457 (t0) REVERT: A 488 ARG cc_start: 0.7791 (mtp180) cc_final: 0.7495 (mtp85) REVERT: A 505 ARG cc_start: 0.8090 (mtt180) cc_final: 0.7878 (mtt180) REVERT: A 633 LYS cc_start: 0.8440 (pttp) cc_final: 0.8092 (pttp) REVERT: A 641 ASP cc_start: 0.7751 (m-30) cc_final: 0.7472 (m-30) REVERT: B 758 GLU cc_start: 0.7278 (tm-30) cc_final: 0.7035 (tm-30) REVERT: B 780 GLU cc_start: 0.7578 (mp0) cc_final: 0.7236 (mp0) REVERT: B 803 GLU cc_start: 0.7977 (tt0) cc_final: 0.7776 (tt0) REVERT: B 822 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7480 (mt-10) REVERT: B 843 GLU cc_start: 0.7863 (tt0) cc_final: 0.7537 (tt0) REVERT: B 894 LEU cc_start: 0.8614 (tp) cc_final: 0.8391 (tt) REVERT: B 904 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8236 (mtpp) REVERT: B 977 GLU cc_start: 0.7648 (tt0) cc_final: 0.7097 (tt0) REVERT: B 982 LEU cc_start: 0.8329 (mm) cc_final: 0.8049 (mp) REVERT: B 1036 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7913 (mtpt) REVERT: B 1153 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7510 (mm-30) REVERT: B 1231 GLU cc_start: 0.7500 (tt0) cc_final: 0.7223 (tt0) REVERT: B 1298 LEU cc_start: 0.8089 (mt) cc_final: 0.7810 (mt) REVERT: B 1362 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7414 (t0) REVERT: B 1364 LYS cc_start: 0.7946 (tttt) cc_final: 0.7637 (tppp) REVERT: B 1420 GLN cc_start: 0.7837 (tm-30) cc_final: 0.7512 (tm-30) REVERT: B 1423 ASN cc_start: 0.7921 (t0) cc_final: 0.7649 (t0) REVERT: B 1433 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7356 (mm-30) REVERT: B 1478 LYS cc_start: 0.8336 (ttpt) cc_final: 0.8109 (tttt) REVERT: B 1512 ARG cc_start: 0.8033 (mtp-110) cc_final: 0.6522 (mtt90) REVERT: B 1513 CYS cc_start: 0.7483 (t) cc_final: 0.7257 (t) REVERT: C 32 LYS cc_start: 0.7962 (pttm) cc_final: 0.7650 (pttm) REVERT: C 37 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7872 (mt-10) REVERT: C 89 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7790 (mtmt) REVERT: C 106 VAL cc_start: 0.8637 (t) cc_final: 0.8236 (p) REVERT: C 123 GLU cc_start: 0.7824 (tp30) cc_final: 0.7518 (tp30) REVERT: C 125 LYS cc_start: 0.8076 (ttmt) cc_final: 0.7817 (ttmt) REVERT: C 126 LYS cc_start: 0.8467 (tttt) cc_final: 0.7752 (tttt) REVERT: C 130 ASP cc_start: 0.7400 (m-30) cc_final: 0.7056 (m-30) REVERT: C 261 TYR cc_start: 0.8156 (t80) cc_final: 0.7927 (t80) REVERT: C 263 GLU cc_start: 0.8127 (tp30) cc_final: 0.7330 (tp30) REVERT: C 267 LYS cc_start: 0.8438 (mmtp) cc_final: 0.7971 (mmtp) REVERT: C 269 LYS cc_start: 0.8273 (tppt) cc_final: 0.7980 (tppt) REVERT: C 272 GLU cc_start: 0.7937 (tt0) cc_final: 0.7527 (tt0) REVERT: C 276 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7315 (mt-10) REVERT: C 288 TYR cc_start: 0.8551 (m-80) cc_final: 0.8120 (m-10) REVERT: C 300 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7794 (mm-30) outliers start: 23 outliers final: 14 residues processed: 437 average time/residue: 0.6965 time to fit residues: 418.9703 Evaluate side-chains 434 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 419 time to evaluate : 2.078 ------------------------------------------------------------------------------- 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 560 VAL Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain B residue 1345 VAL Chi-restraints excluded: chain B residue 1348 TYR 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 286 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 114 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 chunk 90 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.108362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.094408 restraints weight = 60284.998| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.30 r_work: 0.3017 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 13313 Z= 0.255 Angle : 0.580 12.917 18040 Z= 0.304 Chirality : 0.046 0.345 2041 Planarity : 0.005 0.055 2324 Dihedral : 4.339 19.408 1782 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.08 % Allowed : 14.80 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.21), residues: 1641 helix: 1.79 (0.25), residues: 421 sheet: 0.69 (0.22), residues: 526 loop : -0.03 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 552 HIS 0.007 0.001 HIS C 282 PHE 0.018 0.002 PHE A 529 TYR 0.022 0.002 TYR B1432 ARG 0.007 0.001 ARG C 279 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 645) hydrogen bonds : angle 5.15912 ( 1815) SS BOND : bond 0.00610 ( 9) SS BOND : angle 3.87057 ( 18) covalent geometry : bond 0.00601 (13304) covalent geometry : angle 0.56692 (18022) *********************** 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 458 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 428 time to evaluate : 1.815 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 52 ASP cc_start: 0.7941 (m-30) cc_final: 0.7554 (m-30) REVERT: A 82 HIS cc_start: 0.8070 (m-70) cc_final: 0.7754 (m170) REVERT: A 154 HIS cc_start: 0.7698 (p90) cc_final: 0.7299 (p90) REVERT: A 175 VAL cc_start: 0.8632 (t) cc_final: 0.8330 (m) REVERT: A 241 LYS cc_start: 0.8571 (ptpt) cc_final: 0.8306 (mttm) REVERT: A 248 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7324 (mm-30) REVERT: A 258 ARG cc_start: 0.8035 (ptp-170) cc_final: 0.7795 (ptm160) REVERT: A 264 LYS cc_start: 0.8373 (mtmt) cc_final: 0.7959 (mtmm) REVERT: A 295 ASP cc_start: 0.7840 (t0) cc_final: 0.7222 (t0) REVERT: A 299 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7380 (mt-10) REVERT: A 399 SER cc_start: 0.8369 (t) cc_final: 0.7947 (m) REVERT: A 421 SER cc_start: 0.8093 (p) cc_final: 0.7863 (p) REVERT: A 435 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7424 (mt-10) REVERT: A 447 SER cc_start: 0.8456 (t) cc_final: 0.8021 (p) REVERT: A 451 ASN cc_start: 0.7999 (t0) cc_final: 0.7570 (t0) REVERT: A 478 ARG cc_start: 0.7805 (ttt90) cc_final: 0.7556 (ttt90) REVERT: A 488 ARG cc_start: 0.7828 (mtp180) cc_final: 0.7575 (mtp85) REVERT: A 502 LYS cc_start: 0.8503 (tttt) cc_final: 0.8273 (tttp) REVERT: A 633 LYS cc_start: 0.8427 (pttp) cc_final: 0.8060 (pttp) REVERT: A 641 ASP cc_start: 0.7730 (m-30) cc_final: 0.7456 (m-30) REVERT: B 780 GLU cc_start: 0.7541 (mp0) cc_final: 0.7212 (mp0) REVERT: B 822 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7505 (mt-10) REVERT: B 843 GLU cc_start: 0.7867 (tt0) cc_final: 0.7565 (tt0) REVERT: B 865 GLU cc_start: 0.8025 (pt0) cc_final: 0.7684 (pt0) REVERT: B 894 LEU cc_start: 0.8621 (tp) cc_final: 0.8400 (tt) REVERT: B 904 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8253 (mtpp) REVERT: B 1096 ASP cc_start: 0.7953 (m-30) cc_final: 0.7511 (p0) REVERT: B 1153 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7508 (mm-30) REVERT: B 1161 GLN cc_start: 0.7747 (mt0) cc_final: 0.7536 (mt0) REVERT: B 1231 GLU cc_start: 0.7489 (tt0) cc_final: 0.7229 (tt0) REVERT: B 1298 LEU cc_start: 0.8136 (mt) cc_final: 0.7881 (mt) REVERT: B 1335 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6917 (mt-10) REVERT: B 1347 MET cc_start: 0.7689 (mtm) cc_final: 0.7350 (mtm) REVERT: B 1362 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7399 (t0) REVERT: B 1364 LYS cc_start: 0.7992 (tttt) cc_final: 0.7654 (tppp) REVERT: B 1420 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7513 (tm-30) REVERT: B 1423 ASN cc_start: 0.7945 (t0) cc_final: 0.7705 (t0) REVERT: B 1433 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7341 (mm-30) REVERT: B 1478 LYS cc_start: 0.8317 (ttpt) cc_final: 0.8102 (tttt) REVERT: B 1513 CYS cc_start: 0.7485 (t) cc_final: 0.7262 (t) REVERT: C 32 LYS cc_start: 0.8011 (pttm) cc_final: 0.7679 (pttm) REVERT: C 37 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7886 (mt-10) REVERT: C 83 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7641 (tm-30) REVERT: C 106 VAL cc_start: 0.8704 (t) cc_final: 0.8315 (p) REVERT: C 123 GLU cc_start: 0.7844 (tp30) cc_final: 0.7550 (tp30) REVERT: C 125 LYS cc_start: 0.8139 (ttmt) cc_final: 0.7864 (ttmt) REVERT: C 126 LYS cc_start: 0.8507 (tttt) cc_final: 0.7768 (tttt) REVERT: C 130 ASP cc_start: 0.7435 (m-30) cc_final: 0.7100 (m-30) REVERT: C 211 TRP cc_start: 0.8531 (m-10) cc_final: 0.8094 (m-10) REVERT: C 261 TYR cc_start: 0.8141 (t80) cc_final: 0.7881 (t80) REVERT: C 263 GLU cc_start: 0.8132 (tp30) cc_final: 0.7290 (tp30) REVERT: C 269 LYS cc_start: 0.8265 (tppt) cc_final: 0.7925 (tppp) REVERT: C 272 GLU cc_start: 0.7938 (tt0) cc_final: 0.7517 (tt0) REVERT: C 276 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7321 (mt-10) REVERT: C 288 TYR cc_start: 0.8611 (m-80) cc_final: 0.8156 (m-10) REVERT: C 300 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7767 (mm-30) outliers start: 30 outliers final: 21 residues processed: 443 average time/residue: 0.6612 time to fit residues: 400.4075 Evaluate side-chains 444 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 422 time to evaluate : 1.866 ------------------------------------------------------------------------------- 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 360 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 580 GLN 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 109 optimal weight: 0.2980 chunk 151 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 140 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN ** B1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3324 r_free = 0.3324 target = 0.106295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.091973 restraints weight = 60841.500| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.36 r_work: 0.3022 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 13313 Z= 0.143 Angle : 0.542 11.827 18040 Z= 0.281 Chirality : 0.044 0.352 2041 Planarity : 0.004 0.054 2324 Dihedral : 4.197 19.506 1782 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.81 % Allowed : 15.50 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.21), residues: 1641 helix: 1.90 (0.25), residues: 423 sheet: 0.79 (0.22), residues: 522 loop : 0.07 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 166 HIS 0.006 0.001 HIS C 282 PHE 0.013 0.001 PHE A 529 TYR 0.022 0.001 TYR B1432 ARG 0.007 0.000 ARG C 279 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 645) hydrogen bonds : angle 4.98732 ( 1815) SS BOND : bond 0.01120 ( 9) SS BOND : angle 3.51781 ( 18) covalent geometry : bond 0.00345 (13304) covalent geometry : angle 0.53081 (18022) *********************** 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 449 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 423 time to evaluate : 2.058 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: 0.7926 (m-30) cc_final: 0.7536 (m-30) REVERT: A 154 HIS cc_start: 0.7702 (p90) cc_final: 0.7319 (p90) REVERT: A 175 VAL cc_start: 0.8605 (t) cc_final: 0.8325 (m) REVERT: A 240 GLU cc_start: 0.7740 (pt0) cc_final: 0.7534 (pt0) REVERT: A 241 LYS cc_start: 0.8582 (ptpt) cc_final: 0.8304 (mttm) REVERT: A 248 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7295 (mm-30) REVERT: A 258 ARG cc_start: 0.8000 (ptp-170) cc_final: 0.7780 (ptm160) REVERT: A 264 LYS cc_start: 0.8338 (mtmt) cc_final: 0.7913 (mtmm) REVERT: A 295 ASP cc_start: 0.7846 (t0) cc_final: 0.7226 (t0) REVERT: A 299 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7369 (mt-10) REVERT: A 342 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7506 (tt0) REVERT: A 399 SER cc_start: 0.8334 (t) cc_final: 0.7964 (m) REVERT: A 421 SER cc_start: 0.8113 (p) cc_final: 0.7888 (p) REVERT: A 451 ASN cc_start: 0.8004 (t0) cc_final: 0.7553 (t0) REVERT: A 488 ARG cc_start: 0.7745 (mtp180) cc_final: 0.7501 (mtp85) REVERT: A 502 LYS cc_start: 0.8427 (tttt) cc_final: 0.8150 (tttm) REVERT: A 633 LYS cc_start: 0.8438 (pttp) cc_final: 0.8124 (pttp) REVERT: A 641 ASP cc_start: 0.7700 (m-30) cc_final: 0.7424 (m-30) REVERT: B 780 GLU cc_start: 0.7542 (mp0) cc_final: 0.7099 (mp0) REVERT: B 822 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7495 (mt-10) REVERT: B 843 GLU cc_start: 0.7883 (tt0) cc_final: 0.7575 (tt0) REVERT: B 894 LEU cc_start: 0.8610 (tp) cc_final: 0.8397 (tt) REVERT: B 904 LYS cc_start: 0.8586 (mtpp) cc_final: 0.8246 (mtpp) REVERT: B 960 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7443 (mm-30) REVERT: B 977 GLU cc_start: 0.7590 (tt0) cc_final: 0.6911 (tm-30) REVERT: B 982 LEU cc_start: 0.8298 (mm) cc_final: 0.8092 (mt) REVERT: B 1096 ASP cc_start: 0.7956 (m-30) cc_final: 0.7645 (p0) REVERT: B 1153 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7461 (mm-30) REVERT: B 1161 GLN cc_start: 0.7709 (mt0) cc_final: 0.7493 (mt0) REVERT: B 1177 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7440 (mt-10) REVERT: B 1231 GLU cc_start: 0.7482 (tt0) cc_final: 0.7230 (tt0) REVERT: B 1281 GLN cc_start: 0.7928 (tp40) cc_final: 0.7677 (tp40) REVERT: B 1335 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6938 (mt-10) REVERT: B 1362 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7399 (t0) REVERT: B 1364 LYS cc_start: 0.7962 (tttt) cc_final: 0.7627 (tppp) REVERT: B 1420 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7530 (tm-30) REVERT: B 1423 ASN cc_start: 0.7926 (t0) cc_final: 0.7693 (t0) REVERT: B 1433 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7371 (mm-30) REVERT: B 1444 LEU cc_start: 0.8199 (tp) cc_final: 0.7916 (tp) REVERT: B 1478 LYS cc_start: 0.8322 (ttpt) cc_final: 0.8109 (tttt) REVERT: B 1513 CYS cc_start: 0.7515 (t) cc_final: 0.7271 (t) REVERT: C 32 LYS cc_start: 0.7948 (pttm) cc_final: 0.7634 (pttm) REVERT: C 37 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7872 (mt-10) REVERT: C 74 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7518 (mm-30) REVERT: C 106 VAL cc_start: 0.8679 (t) cc_final: 0.8267 (p) REVERT: C 107 LYS cc_start: 0.8495 (mmtt) cc_final: 0.7902 (mmtt) REVERT: C 123 GLU cc_start: 0.7816 (tp30) cc_final: 0.7519 (tp30) REVERT: C 125 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7852 (ttmt) REVERT: C 126 LYS cc_start: 0.8485 (tttt) cc_final: 0.7749 (tttt) REVERT: C 130 ASP cc_start: 0.7427 (m-30) cc_final: 0.7077 (m-30) REVERT: C 211 TRP cc_start: 0.8513 (m-10) cc_final: 0.7785 (m-10) REVERT: C 263 GLU cc_start: 0.8114 (tp30) cc_final: 0.7268 (tp30) REVERT: C 269 LYS cc_start: 0.8250 (tppt) cc_final: 0.7912 (tppp) REVERT: C 272 GLU cc_start: 0.7933 (tt0) cc_final: 0.7501 (tt0) REVERT: C 276 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7271 (mt-10) REVERT: C 288 TYR cc_start: 0.8611 (m-80) cc_final: 0.8186 (m-10) REVERT: C 300 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7737 (mm-30) outliers start: 26 outliers final: 20 residues processed: 434 average time/residue: 0.6931 time to fit residues: 413.0429 Evaluate side-chains 440 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 419 time to evaluate : 2.110 ------------------------------------------------------------------------------- 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 327 SER Chi-restraints excluded: chain A residue 377 THR 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 1345 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 163 optimal weight: 0.5980 chunk 151 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 161 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3321 r_free = 0.3321 target = 0.106345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.092315 restraints weight = 60901.805| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.32 r_work: 0.3008 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3512 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= 0.197 Angle : 0.557 12.531 18040 Z= 0.289 Chirality : 0.044 0.412 2041 Planarity : 0.004 0.053 2324 Dihedral : 4.207 19.261 1782 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.95 % Allowed : 15.22 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.21), residues: 1641 helix: 1.83 (0.25), residues: 423 sheet: 0.79 (0.22), residues: 521 loop : 0.03 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 166 HIS 0.005 0.001 HIS C 282 PHE 0.015 0.002 PHE A 529 TYR 0.019 0.002 TYR B1432 ARG 0.008 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 645) hydrogen bonds : angle 4.90734 ( 1815) SS BOND : bond 0.01414 ( 9) SS BOND : angle 3.83238 ( 18) covalent geometry : bond 0.00472 (13304) covalent geometry : angle 0.54363 (18022) *********************** 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: 28 poor density : 432 time to evaluate : 2.252 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: 0.7961 (m-30) cc_final: 0.7574 (m-30) REVERT: A 175 VAL cc_start: 0.8620 (t) cc_final: 0.8350 (m) REVERT: A 237 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7263 (mm-30) REVERT: A 241 LYS cc_start: 0.8588 (ptpt) cc_final: 0.8315 (mttm) REVERT: A 248 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7287 (mm-30) REVERT: A 258 ARG cc_start: 0.8008 (ptp-170) cc_final: 0.7792 (ptm160) REVERT: A 264 LYS cc_start: 0.8333 (mtmt) cc_final: 0.7922 (mtmm) REVERT: A 295 ASP cc_start: 0.7846 (t0) cc_final: 0.7222 (t0) REVERT: A 299 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7318 (mt-10) REVERT: A 342 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7527 (tt0) REVERT: A 387 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8219 (m) REVERT: A 399 SER cc_start: 0.8316 (t) cc_final: 0.7943 (m) REVERT: A 412 ASN cc_start: 0.8073 (m110) cc_final: 0.7860 (m-40) REVERT: A 421 SER cc_start: 0.8095 (p) cc_final: 0.7875 (p) REVERT: A 435 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7426 (mt-10) REVERT: A 447 SER cc_start: 0.8432 (t) cc_final: 0.7992 (p) REVERT: A 451 ASN cc_start: 0.8023 (t0) cc_final: 0.7591 (t0) REVERT: A 488 ARG cc_start: 0.7822 (mtp180) cc_final: 0.7583 (mtp85) REVERT: A 502 LYS cc_start: 0.8440 (tttt) cc_final: 0.8152 (tttm) REVERT: A 608 LYS cc_start: 0.8272 (mtmm) cc_final: 0.7972 (mtmm) REVERT: A 633 LYS cc_start: 0.8435 (pttp) cc_final: 0.8019 (pttp) REVERT: A 641 ASP cc_start: 0.7719 (m-30) cc_final: 0.7471 (m-30) REVERT: B 780 GLU cc_start: 0.7546 (mp0) cc_final: 0.7089 (mp0) REVERT: B 822 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7467 (mt-10) REVERT: B 843 GLU cc_start: 0.7848 (tt0) cc_final: 0.7552 (tt0) REVERT: B 894 LEU cc_start: 0.8614 (tp) cc_final: 0.8400 (tt) REVERT: B 904 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8228 (mtpp) REVERT: B 960 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7309 (mm-30) REVERT: B 977 GLU cc_start: 0.7573 (tt0) cc_final: 0.6981 (tm-30) REVERT: B 982 LEU cc_start: 0.8274 (mm) cc_final: 0.8067 (mt) REVERT: B 1096 ASP cc_start: 0.7945 (m-30) cc_final: 0.7691 (p0) REVERT: B 1153 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7491 (mm-30) REVERT: B 1177 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7468 (mt-10) REVERT: B 1231 GLU cc_start: 0.7475 (tt0) cc_final: 0.7227 (tt0) REVERT: B 1335 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6972 (mt-10) REVERT: B 1362 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7378 (t0) REVERT: B 1364 LYS cc_start: 0.7979 (tttt) cc_final: 0.7657 (tppp) REVERT: B 1420 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7543 (tm-30) REVERT: B 1423 ASN cc_start: 0.7953 (t0) cc_final: 0.7733 (t0) REVERT: B 1433 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7370 (mm-30) REVERT: B 1478 LYS cc_start: 0.8347 (ttpt) cc_final: 0.8146 (tttt) REVERT: B 1513 CYS cc_start: 0.7509 (t) cc_final: 0.7283 (t) REVERT: C 32 LYS cc_start: 0.7960 (pttm) cc_final: 0.7642 (pttm) REVERT: C 37 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7897 (mt-10) REVERT: C 74 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7521 (mm-30) REVERT: C 83 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7513 (tm-30) REVERT: C 104 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7552 (mm-30) REVERT: C 106 VAL cc_start: 0.8714 (t) cc_final: 0.8311 (p) REVERT: C 107 LYS cc_start: 0.8510 (mmtt) cc_final: 0.7915 (mmtt) REVERT: C 125 LYS cc_start: 0.8126 (ttmt) cc_final: 0.7845 (ttmt) REVERT: C 126 LYS cc_start: 0.8497 (tttt) cc_final: 0.7771 (tttt) REVERT: C 130 ASP cc_start: 0.7442 (m-30) cc_final: 0.7092 (m-30) REVERT: C 211 TRP cc_start: 0.8538 (m-10) cc_final: 0.7821 (m-10) REVERT: C 263 GLU cc_start: 0.8100 (tp30) cc_final: 0.7298 (tp30) REVERT: C 269 LYS cc_start: 0.8242 (tppt) cc_final: 0.7909 (tppp) REVERT: C 272 GLU cc_start: 0.7941 (tt0) cc_final: 0.7461 (tt0) REVERT: C 276 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7272 (mt-10) REVERT: C 288 TYR cc_start: 0.8631 (m-80) cc_final: 0.8147 (m-10) REVERT: C 300 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7745 (mm-30) outliers start: 28 outliers final: 22 residues processed: 443 average time/residue: 0.6840 time to fit residues: 414.8846 Evaluate side-chains 453 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 429 time to evaluate : 1.981 ------------------------------------------------------------------------------- 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 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 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 1345 VAL 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 1426 ASP Chi-restraints excluded: chain B residue 1453 HIS Chi-restraints excluded: chain B residue 1505 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 148 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 79 optimal weight: 0.0980 chunk 27 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.105743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.091675 restraints weight = 61041.580| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.33 r_work: 0.3007 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 13313 Z= 0.194 Angle : 0.557 10.464 18040 Z= 0.289 Chirality : 0.044 0.327 2041 Planarity : 0.004 0.041 2324 Dihedral : 4.225 19.914 1782 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.15 % Allowed : 15.43 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.21), residues: 1641 helix: 1.82 (0.25), residues: 423 sheet: 0.78 (0.22), residues: 523 loop : -0.03 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 166 HIS 0.005 0.001 HIS C 282 PHE 0.016 0.002 PHE A 529 TYR 0.018 0.002 TYR B1432 ARG 0.010 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 645) hydrogen bonds : angle 4.87631 ( 1815) SS BOND : bond 0.00942 ( 9) SS BOND : angle 3.27471 ( 18) covalent geometry : bond 0.00459 (13304) covalent geometry : angle 0.54759 (18022) *********************** 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 467 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 436 time to evaluate : 2.193 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: 0.7937 (m-30) cc_final: 0.7545 (m-30) REVERT: A 175 VAL cc_start: 0.8610 (t) cc_final: 0.8341 (m) REVERT: A 237 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7346 (mm-30) REVERT: A 241 LYS cc_start: 0.8591 (ptpt) cc_final: 0.8308 (mttm) REVERT: A 248 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7333 (mm-30) REVERT: A 258 ARG cc_start: 0.8008 (ptp-170) cc_final: 0.7786 (ptm160) REVERT: A 295 ASP cc_start: 0.7870 (t0) cc_final: 0.7260 (t0) REVERT: A 299 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7349 (mt-10) REVERT: A 342 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7504 (tt0) REVERT: A 387 VAL cc_start: 0.8486 (OUTLIER) cc_final: 0.8190 (m) REVERT: A 399 SER cc_start: 0.8338 (t) cc_final: 0.7954 (m) REVERT: A 412 ASN cc_start: 0.8106 (m110) cc_final: 0.7886 (t0) REVERT: A 421 SER cc_start: 0.8089 (p) cc_final: 0.7868 (p) REVERT: A 435 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7439 (mt-10) REVERT: A 447 SER cc_start: 0.8433 (t) cc_final: 0.7987 (p) REVERT: A 451 ASN cc_start: 0.8039 (t0) cc_final: 0.7604 (t0) REVERT: A 488 ARG cc_start: 0.7816 (mtp180) cc_final: 0.7576 (mtp85) REVERT: A 502 LYS cc_start: 0.8417 (tttt) cc_final: 0.8189 (tttp) REVERT: A 505 ARG cc_start: 0.8143 (mtt180) cc_final: 0.7860 (mtt180) REVERT: A 519 LEU cc_start: 0.7665 (tp) cc_final: 0.7393 (tt) REVERT: A 633 LYS cc_start: 0.8404 (pttp) cc_final: 0.7975 (pttp) REVERT: A 641 ASP cc_start: 0.7739 (m-30) cc_final: 0.7501 (m-30) REVERT: B 780 GLU cc_start: 0.7560 (mp0) cc_final: 0.7104 (mp0) REVERT: B 783 LYS cc_start: 0.8210 (mttm) cc_final: 0.7957 (mttm) REVERT: B 822 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7504 (mt-10) REVERT: B 843 GLU cc_start: 0.7886 (tt0) cc_final: 0.7583 (tt0) REVERT: B 894 LEU cc_start: 0.8615 (tp) cc_final: 0.8341 (tt) REVERT: B 904 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8245 (mtpp) REVERT: B 960 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7181 (mm-30) REVERT: B 977 GLU cc_start: 0.7543 (tt0) cc_final: 0.6973 (tm-30) REVERT: B 982 LEU cc_start: 0.8247 (mm) cc_final: 0.8045 (mt) REVERT: B 1153 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7413 (mm-30) REVERT: B 1177 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7485 (mt-10) REVERT: B 1231 GLU cc_start: 0.7468 (tt0) cc_final: 0.7142 (tt0) REVERT: B 1333 THR cc_start: 0.8154 (m) cc_final: 0.7541 (p) REVERT: B 1335 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6839 (mt-10) REVERT: B 1345 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.8088 (t) REVERT: B 1362 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7384 (t0) REVERT: B 1364 LYS cc_start: 0.7994 (tttt) cc_final: 0.7683 (tppp) REVERT: B 1383 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8517 (p) REVERT: B 1420 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7515 (tm-30) REVERT: B 1423 ASN cc_start: 0.7947 (t0) cc_final: 0.7725 (t0) REVERT: B 1433 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7362 (mm-30) REVERT: B 1478 LYS cc_start: 0.8349 (ttpt) cc_final: 0.8141 (tttt) REVERT: C 32 LYS cc_start: 0.7966 (pttm) cc_final: 0.7653 (pttm) REVERT: C 37 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7903 (mt-10) REVERT: C 74 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7516 (mm-30) REVERT: C 83 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7525 (tm-30) REVERT: C 104 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7564 (mm-30) REVERT: C 106 VAL cc_start: 0.8731 (t) cc_final: 0.8336 (p) REVERT: C 107 LYS cc_start: 0.8534 (mmtt) cc_final: 0.7925 (mmtt) REVERT: C 123 GLU cc_start: 0.7793 (tp30) cc_final: 0.7537 (tp30) REVERT: C 125 LYS cc_start: 0.8129 (ttmt) cc_final: 0.7836 (ttmt) REVERT: C 126 LYS cc_start: 0.8499 (tttt) cc_final: 0.7760 (tttt) REVERT: C 130 ASP cc_start: 0.7457 (m-30) cc_final: 0.7155 (m-30) REVERT: C 211 TRP cc_start: 0.8423 (m-10) cc_final: 0.7697 (m-10) REVERT: C 269 LYS cc_start: 0.8286 (tppt) cc_final: 0.7918 (tppp) REVERT: C 272 GLU cc_start: 0.7917 (tt0) cc_final: 0.7426 (tt0) REVERT: C 276 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7262 (mt-10) REVERT: C 277 LYS cc_start: 0.8019 (mttm) cc_final: 0.7411 (mtmm) REVERT: C 288 TYR cc_start: 0.8640 (m-80) cc_final: 0.8151 (m-10) REVERT: C 300 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7722 (mm-30) outliers start: 31 outliers final: 22 residues processed: 447 average time/residue: 0.7249 time to fit residues: 446.6435 Evaluate side-chains 455 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 429 time to evaluate : 1.827 ------------------------------------------------------------------------------- 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 60 HIS Chi-restraints excluded: chain A residue 65 LYS 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 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 769 GLU Chi-restraints excluded: chain B residue 859 GLU Chi-restraints excluded: chain B residue 1110 GLU Chi-restraints excluded: chain B residue 1345 VAL 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 1426 ASP Chi-restraints excluded: chain B residue 1453 HIS Chi-restraints excluded: chain B residue 1505 LEU 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 29 optimal weight: 0.0270 chunk 22 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 34 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 86 optimal weight: 0.0020 chunk 77 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 overall best weight: 0.3846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3354 r_free = 0.3354 target = 0.108383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.094262 restraints weight = 60513.587| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.33 r_work: 0.3045 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.149 13313 Z= 0.124 Angle : 0.540 11.334 18040 Z= 0.278 Chirality : 0.044 0.373 2041 Planarity : 0.004 0.039 2324 Dihedral : 4.106 20.817 1782 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.95 % Allowed : 15.84 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.21), residues: 1641 helix: 1.98 (0.25), residues: 423 sheet: 0.84 (0.22), residues: 523 loop : 0.06 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 211 HIS 0.004 0.001 HIS C 282 PHE 0.011 0.001 PHE A 529 TYR 0.017 0.001 TYR B1432 ARG 0.010 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 645) hydrogen bonds : angle 4.72322 ( 1815) SS BOND : bond 0.01221 ( 9) SS BOND : angle 3.66906 ( 18) covalent geometry : bond 0.00304 (13304) covalent geometry : angle 0.52791 (18022) *********************** 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 459 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 431 time to evaluate : 2.058 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: symmetry clash REVERT: A 52 ASP cc_start: 0.7923 (m-30) cc_final: 0.7531 (m-30) REVERT: A 175 VAL cc_start: 0.8607 (t) cc_final: 0.8351 (m) REVERT: A 237 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7315 (mm-30) REVERT: A 241 LYS cc_start: 0.8598 (ptpt) cc_final: 0.8308 (mttm) REVERT: A 248 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7342 (mm-30) REVERT: A 264 LYS cc_start: 0.8251 (mtmt) cc_final: 0.7979 (mtmm) REVERT: A 299 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7346 (mt-10) REVERT: A 342 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7502 (tt0) REVERT: A 387 VAL cc_start: 0.8527 (OUTLIER) cc_final: 0.8222 (m) REVERT: A 399 SER cc_start: 0.8340 (t) cc_final: 0.7963 (m) REVERT: A 412 ASN cc_start: 0.8073 (m110) cc_final: 0.7857 (t0) REVERT: A 421 SER cc_start: 0.8083 (p) cc_final: 0.7877 (p) REVERT: A 435 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7406 (mt-10) REVERT: A 447 SER cc_start: 0.8383 (t) cc_final: 0.7949 (p) REVERT: A 451 ASN cc_start: 0.8022 (t0) cc_final: 0.7610 (t0) REVERT: A 488 ARG cc_start: 0.7753 (mtp180) cc_final: 0.7457 (mtp85) REVERT: A 502 LYS cc_start: 0.8412 (tttt) cc_final: 0.8102 (tttm) REVERT: A 505 ARG cc_start: 0.8085 (mtt180) cc_final: 0.7840 (mtt180) REVERT: A 633 LYS cc_start: 0.8382 (pttp) cc_final: 0.7951 (pttp) REVERT: A 641 ASP cc_start: 0.7679 (m-30) cc_final: 0.7422 (m-30) REVERT: B 780 GLU cc_start: 0.7527 (mp0) cc_final: 0.7098 (mp0) REVERT: B 783 LYS cc_start: 0.8160 (mttm) cc_final: 0.7902 (mttm) REVERT: B 822 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7488 (mt-10) REVERT: B 843 GLU cc_start: 0.7856 (tt0) cc_final: 0.7552 (tt0) REVERT: B 894 LEU cc_start: 0.8602 (tp) cc_final: 0.8334 (tt) REVERT: B 904 LYS cc_start: 0.8594 (mtpp) cc_final: 0.8218 (mtpp) REVERT: B 977 GLU cc_start: 0.7568 (tt0) cc_final: 0.6981 (tm-30) REVERT: B 1153 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7454 (mm-30) REVERT: B 1231 GLU cc_start: 0.7433 (tt0) cc_final: 0.7106 (tt0) REVERT: B 1362 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7375 (t0) REVERT: B 1364 LYS cc_start: 0.7958 (tttt) cc_final: 0.7647 (tppp) REVERT: B 1383 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8523 (p) REVERT: B 1420 GLN cc_start: 0.7879 (tm-30) cc_final: 0.7534 (tm-30) REVERT: B 1423 ASN cc_start: 0.7930 (t0) cc_final: 0.7706 (t0) REVERT: B 1433 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7375 (mm-30) REVERT: B 1478 LYS cc_start: 0.8331 (ttpt) cc_final: 0.8121 (tttt) REVERT: C 32 LYS cc_start: 0.7913 (pttm) cc_final: 0.7606 (pttm) REVERT: C 37 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7888 (mt-10) REVERT: C 74 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7538 (mm-30) REVERT: C 83 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7504 (tm-30) REVERT: C 84 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8222 (mtpt) REVERT: C 104 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7519 (mm-30) REVERT: C 106 VAL cc_start: 0.8706 (t) cc_final: 0.8308 (p) REVERT: C 107 LYS cc_start: 0.8497 (mmtt) cc_final: 0.7890 (mmtt) REVERT: C 123 GLU cc_start: 0.7767 (tp30) cc_final: 0.7500 (tp30) REVERT: C 125 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7841 (ttmt) REVERT: C 126 LYS cc_start: 0.8481 (tttt) cc_final: 0.7760 (tttt) REVERT: C 130 ASP cc_start: 0.7452 (m-30) cc_final: 0.7100 (m-30) REVERT: C 211 TRP cc_start: 0.8372 (m-10) cc_final: 0.7698 (m-10) REVERT: C 269 LYS cc_start: 0.8291 (tppt) cc_final: 0.7922 (tppp) REVERT: C 272 GLU cc_start: 0.7917 (tt0) cc_final: 0.7417 (tt0) REVERT: C 276 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7202 (mt-10) REVERT: C 288 TYR cc_start: 0.8594 (m-80) cc_final: 0.8155 (m-10) outliers start: 28 outliers final: 19 residues processed: 444 average time/residue: 0.7032 time to fit residues: 430.0999 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 : 1.890 ------------------------------------------------------------------------------- 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 60 HIS Chi-restraints excluded: chain A residue 65 LYS 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 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 1505 LEU 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 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3318 r_free = 0.3318 target = 0.105924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.091951 restraints weight = 60602.261| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.32 r_work: 0.3034 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.136 13313 Z= 0.188 Angle : 0.557 10.481 18040 Z= 0.289 Chirality : 0.044 0.360 2041 Planarity : 0.004 0.037 2324 Dihedral : 4.158 20.992 1782 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.60 % Allowed : 16.33 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.21), residues: 1641 helix: 1.92 (0.25), residues: 423 sheet: 0.83 (0.22), residues: 522 loop : 0.01 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 211 HIS 0.004 0.001 HIS C 282 PHE 0.016 0.002 PHE B1037 TYR 0.022 0.002 TYR A 261 ARG 0.014 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 645) hydrogen bonds : angle 4.74146 ( 1815) SS BOND : bond 0.01049 ( 9) SS BOND : angle 3.47987 ( 18) covalent geometry : bond 0.00450 (13304) covalent geometry : angle 0.54656 (18022) ********************** 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 455 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 432 time to evaluate : 1.901 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: 0.7918 (m-30) cc_final: 0.7518 (m-30) REVERT: A 175 VAL cc_start: 0.8611 (t) cc_final: 0.8357 (m) REVERT: A 237 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7355 (mm-30) REVERT: A 240 GLU cc_start: 0.7606 (pt0) cc_final: 0.7277 (pm20) REVERT: A 241 LYS cc_start: 0.8586 (ptpt) cc_final: 0.8311 (mttm) REVERT: A 248 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7349 (mm-30) REVERT: A 299 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7346 (mt-10) REVERT: A 342 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7507 (tt0) REVERT: A 387 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8240 (m) REVERT: A 399 SER cc_start: 0.8330 (t) cc_final: 0.7956 (m) REVERT: A 412 ASN cc_start: 0.8091 (m110) cc_final: 0.7870 (t0) REVERT: A 435 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7426 (mt-10) REVERT: A 447 SER cc_start: 0.8376 (t) cc_final: 0.7925 (p) REVERT: A 451 ASN cc_start: 0.8046 (t0) cc_final: 0.7608 (t0) REVERT: A 488 ARG cc_start: 0.7796 (mtp180) cc_final: 0.7485 (mtp85) REVERT: A 502 LYS cc_start: 0.8410 (tttt) cc_final: 0.8171 (tttp) REVERT: A 505 ARG cc_start: 0.8131 (mtt180) cc_final: 0.7901 (mtt180) REVERT: A 633 LYS cc_start: 0.8347 (pttp) cc_final: 0.7919 (pttp) REVERT: A 641 ASP cc_start: 0.7714 (m-30) cc_final: 0.7472 (m-30) REVERT: B 780 GLU cc_start: 0.7534 (mp0) cc_final: 0.7095 (mp0) REVERT: B 822 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7506 (mt-10) REVERT: B 843 GLU cc_start: 0.7880 (tt0) cc_final: 0.7570 (tt0) REVERT: B 894 LEU cc_start: 0.8613 (tp) cc_final: 0.8337 (tt) REVERT: B 904 LYS cc_start: 0.8603 (mtpp) cc_final: 0.8218 (mtpp) REVERT: B 977 GLU cc_start: 0.7532 (tt0) cc_final: 0.6957 (tm-30) REVERT: B 1153 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7459 (mm-30) REVERT: B 1231 GLU cc_start: 0.7466 (tt0) cc_final: 0.7222 (tt0) REVERT: B 1298 LEU cc_start: 0.8152 (mp) cc_final: 0.7892 (mt) REVERT: B 1333 THR cc_start: 0.8157 (m) cc_final: 0.7561 (p) REVERT: B 1362 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7377 (t0) REVERT: B 1364 LYS cc_start: 0.7988 (tttt) cc_final: 0.7653 (tppp) REVERT: B 1383 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8522 (p) REVERT: B 1420 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7525 (tm-30) REVERT: B 1423 ASN cc_start: 0.7919 (t0) cc_final: 0.7693 (t0) REVERT: B 1433 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7369 (mm-30) REVERT: B 1478 LYS cc_start: 0.8372 (ttpt) cc_final: 0.8157 (tttt) REVERT: C 32 LYS cc_start: 0.7927 (pttm) cc_final: 0.7609 (pttm) REVERT: C 37 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7937 (mt-10) REVERT: C 74 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7533 (mm-30) REVERT: C 83 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7522 (tm-30) REVERT: C 84 LYS cc_start: 0.8621 (mtpt) cc_final: 0.8215 (mtpt) REVERT: C 104 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7579 (mm-30) REVERT: C 106 VAL cc_start: 0.8733 (t) cc_final: 0.8340 (p) REVERT: C 107 LYS cc_start: 0.8532 (mmtt) cc_final: 0.7916 (mmtt) REVERT: C 123 GLU cc_start: 0.7778 (tp30) cc_final: 0.7530 (tp30) REVERT: C 125 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7853 (ttmt) REVERT: C 126 LYS cc_start: 0.8497 (tttt) cc_final: 0.7772 (tttt) REVERT: C 130 ASP cc_start: 0.7473 (m-30) cc_final: 0.7173 (m-30) REVERT: C 211 TRP cc_start: 0.8434 (m-10) cc_final: 0.7742 (m-10) REVERT: C 269 LYS cc_start: 0.8280 (tppt) cc_final: 0.7914 (tppp) REVERT: C 272 GLU cc_start: 0.7947 (tt0) cc_final: 0.7429 (tt0) REVERT: C 276 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7215 (mt-10) REVERT: C 277 LYS cc_start: 0.8018 (mttm) cc_final: 0.7428 (mtmm) REVERT: C 288 TYR cc_start: 0.8608 (m-80) cc_final: 0.8170 (m-10) outliers start: 23 outliers final: 17 residues processed: 441 average time/residue: 0.6834 time to fit residues: 413.2342 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 : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 65 LYS 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 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 859 GLU Chi-restraints excluded: chain B residue 1110 GLU 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 1426 ASP Chi-restraints excluded: chain B residue 1453 HIS Chi-restraints excluded: chain B residue 1505 LEU Chi-restraints excluded: chain C residue 188 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 144 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3303 r_free = 0.3303 target = 0.105014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.090976 restraints weight = 60927.735| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.34 r_work: 0.3013 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 13313 Z= 0.186 Angle : 0.557 10.129 18040 Z= 0.288 Chirality : 0.044 0.342 2041 Planarity : 0.004 0.037 2324 Dihedral : 4.176 20.931 1782 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.60 % Allowed : 16.47 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1641 helix: 1.87 (0.25), residues: 423 sheet: 0.83 (0.22), residues: 523 loop : -0.02 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 166 HIS 0.004 0.001 HIS C 282 PHE 0.016 0.002 PHE A 529 TYR 0.018 0.002 TYR A 261 ARG 0.014 0.000 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 645) hydrogen bonds : angle 4.73219 ( 1815) SS BOND : bond 0.00928 ( 9) SS BOND : angle 3.28510 ( 18) covalent geometry : bond 0.00442 (13304) covalent geometry : angle 0.54797 (18022) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13634.84 seconds wall clock time: 234 minutes 2.88 seconds (14042.88 seconds total)