Starting phenix.real_space_refine on Fri Apr 12 15:07:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovb_17209/04_2024/8ovb_17209.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovb_17209/04_2024/8ovb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovb_17209/04_2024/8ovb_17209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovb_17209/04_2024/8ovb_17209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovb_17209/04_2024/8ovb_17209.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovb_17209/04_2024/8ovb_17209.pdb" } 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 Residue "A GLU 39": "OE1" <-> "OE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1066": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1361": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1395": "OD1" <-> "OD2" Residue "B TYR 1466": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 11.02, per 1000 atoms: 0.42 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 - 3.50 Amino acid : False - 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: 20.93 Conformation dependent library (CDL) restraints added in 2.7 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: 2.07 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: 12.22 Time building geometry restraints manager: 21.70 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: 99.32 - 106.25: 362 106.25 - 113.19: 31605 113.19 - 120.12: 7879 120.12 - 127.06: 7832 127.06 - 133.99: 145 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 1.850 nonbonded pdb=" OE1 GLN B 856 " pdb=" H GLN B 856 " model vdw 1.595 1.850 nonbonded pdb=" H SER B1452 " pdb=" OD2 ASP B1457 " model vdw 1.610 1.850 nonbonded pdb="HH11 ARG A 102 " pdb=" OE1 GLU B1032 " model vdw 1.613 1.850 nonbonded pdb="HH12 ARG B 848 " pdb=" OD2 ASP B1404 " model vdw 1.624 1.850 ... (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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 0.400 Extract box with map and model: 9.140 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 86.290 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.090 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: 0.100 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.060 ------------------------------------------------------------------------------- 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 13304 Z= 0.248 Angle : 0.519 10.867 18022 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 490 time to evaluate : 1.984 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: 0.6999 time to fit residues: 477.0708 Evaluate side-chains 445 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 2.212 ------------------------------------------------------------------------------- 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: 0.3980 chunk 124 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 A 569 GLN ** B1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1465 GLN C 66 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13304 Z= 0.329 Angle : 0.559 6.068 18022 Z= 0.301 Chirality : 0.045 0.197 2041 Planarity : 0.004 0.051 2324 Dihedral : 4.147 18.066 1782 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.25 % Allowed : 11.05 % Favored : 87.70 % 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: 1.60 (0.21), residues: 1641 helix: 2.35 (0.26), residues: 423 sheet: 0.97 (0.22), residues: 531 loop : 0.42 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 81 HIS 0.009 0.001 HIS C 282 PHE 0.018 0.002 PHE A 529 TYR 0.016 0.002 TYR A 147 ARG 0.006 0.001 ARG C 56 *********************** 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 495 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 477 time to evaluate : 2.695 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: 0.7419 (m-30) cc_final: 0.6975 (m-30) REVERT: A 72 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6973 (mm-30) REVERT: A 82 HIS cc_start: 0.7085 (m-70) cc_final: 0.6733 (m170) REVERT: A 154 HIS cc_start: 0.7450 (p90) cc_final: 0.7006 (p90) REVERT: A 169 ASN cc_start: 0.7216 (t0) cc_final: 0.6990 (m-40) REVERT: A 226 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7073 (mt-10) REVERT: A 237 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6761 (mm-30) REVERT: A 240 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6789 (pm20) REVERT: A 241 LYS cc_start: 0.8006 (ptpt) cc_final: 0.7682 (mttm) REVERT: A 246 TYR cc_start: 0.7509 (m-80) cc_final: 0.7308 (m-80) REVERT: A 248 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7210 (mm-30) REVERT: A 254 THR cc_start: 0.7758 (m) cc_final: 0.7417 (p) REVERT: A 258 ARG cc_start: 0.7365 (ptp-170) cc_final: 0.7019 (ptp-110) REVERT: A 264 LYS cc_start: 0.7388 (mtmt) cc_final: 0.7044 (mtmm) REVERT: A 286 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7459 (mm-30) REVERT: A 295 ASP cc_start: 0.7367 (t0) cc_final: 0.6812 (t0) REVERT: A 299 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7002 (mt-10) REVERT: A 399 SER cc_start: 0.7919 (t) cc_final: 0.7362 (m) REVERT: A 435 GLU cc_start: 0.6574 (mt-10) cc_final: 0.6322 (mt-10) REVERT: A 451 ASN cc_start: 0.7070 (t0) cc_final: 0.6658 (t0) REVERT: A 488 ARG cc_start: 0.7315 (mtp180) cc_final: 0.6959 (mtp85) REVERT: A 489 TYR cc_start: 0.8199 (p90) cc_final: 0.7887 (p90) REVERT: A 505 ARG cc_start: 0.7825 (mtt180) cc_final: 0.7353 (mtt180) REVERT: A 509 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6908 (mm-30) REVERT: A 514 LEU cc_start: 0.7624 (tt) cc_final: 0.7323 (tp) REVERT: A 634 ASP cc_start: 0.6643 (p0) cc_final: 0.6437 (p0) REVERT: A 641 ASP cc_start: 0.7648 (m-30) cc_final: 0.7393 (m-30) REVERT: B 776 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6439 (mm-30) REVERT: B 803 GLU cc_start: 0.7645 (tt0) cc_final: 0.7331 (tt0) REVERT: B 828 ASP cc_start: 0.7723 (m-30) cc_final: 0.7438 (m-30) REVERT: B 843 GLU cc_start: 0.7503 (tt0) cc_final: 0.6904 (tt0) REVERT: B 894 LEU cc_start: 0.7362 (tp) cc_final: 0.7155 (tt) REVERT: B 904 LYS cc_start: 0.7849 (mtpp) cc_final: 0.7382 (mttp) REVERT: B 933 PRO cc_start: 0.8252 (Cg_exo) cc_final: 0.7974 (Cg_endo) REVERT: B 977 GLU cc_start: 0.6760 (tt0) cc_final: 0.6232 (tt0) REVERT: B 1033 GLN cc_start: 0.6275 (mm-40) cc_final: 0.5919 (mt0) REVERT: B 1035 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7130 (mt-10) REVERT: B 1186 SER cc_start: 0.5983 (m) cc_final: 0.5378 (t) REVERT: B 1298 LEU cc_start: 0.5993 (mt) cc_final: 0.5739 (mt) REVERT: B 1310 ARG cc_start: 0.6966 (mtp-110) cc_final: 0.6765 (mtp-110) REVERT: B 1325 LYS cc_start: 0.7397 (mmmm) cc_final: 0.6903 (mmmm) REVERT: B 1348 TYR cc_start: 0.6830 (p90) cc_final: 0.6534 (p90) REVERT: B 1360 LYS cc_start: 0.6728 (mmtm) cc_final: 0.6387 (mmmm) REVERT: B 1362 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6715 (t0) REVERT: B 1364 LYS cc_start: 0.7359 (tttt) cc_final: 0.6680 (tppp) REVERT: B 1411 PHE cc_start: 0.7256 (m-80) cc_final: 0.6960 (m-80) REVERT: B 1420 GLN cc_start: 0.6826 (tm-30) cc_final: 0.6509 (tm-30) REVERT: B 1423 ASN cc_start: 0.6811 (t0) cc_final: 0.6585 (t0) REVERT: B 1433 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6900 (mm-30) REVERT: B 1457 ASP cc_start: 0.6087 (m-30) cc_final: 0.5771 (p0) REVERT: B 1478 LYS cc_start: 0.7293 (ttpt) cc_final: 0.6915 (tttt) REVERT: B 1487 GLU cc_start: 0.6812 (tt0) cc_final: 0.6389 (tt0) REVERT: B 1512 ARG cc_start: 0.5825 (mtp-110) cc_final: 0.4523 (mtt90) REVERT: B 1513 CYS cc_start: 0.6303 (t) cc_final: 0.6033 (t) REVERT: C 32 LYS cc_start: 0.7506 (pttm) cc_final: 0.7138 (pttm) REVERT: C 33 ASN cc_start: 0.7308 (m-40) cc_final: 0.6838 (m-40) REVERT: C 37 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7686 (mt-10) REVERT: C 89 LYS cc_start: 0.7839 (mtmt) cc_final: 0.7597 (mtmt) REVERT: C 106 VAL cc_start: 0.8039 (t) cc_final: 0.7659 (p) REVERT: C 123 GLU cc_start: 0.7757 (tp30) cc_final: 0.7355 (tp30) REVERT: C 125 LYS cc_start: 0.7388 (ttmt) cc_final: 0.7150 (ttmt) REVERT: C 126 LYS cc_start: 0.8073 (tttt) cc_final: 0.7327 (tttt) REVERT: C 130 ASP cc_start: 0.6942 (m-30) cc_final: 0.6574 (m-30) REVERT: C 255 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7487 (mt-10) REVERT: C 263 GLU cc_start: 0.7722 (tp30) cc_final: 0.7003 (tp30) REVERT: C 267 LYS cc_start: 0.7805 (mmtp) cc_final: 0.7433 (mmtp) REVERT: C 269 LYS cc_start: 0.7748 (tppt) cc_final: 0.7512 (tppt) REVERT: C 272 GLU cc_start: 0.7651 (tt0) cc_final: 0.7267 (tt0) REVERT: C 276 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6973 (mt-10) REVERT: C 277 LYS cc_start: 0.7430 (mttm) cc_final: 0.7204 (mttm) outliers start: 18 outliers final: 11 residues processed: 481 average time/residue: 0.7055 time to fit residues: 469.8710 Evaluate side-chains 460 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 448 time to evaluate : 2.224 ------------------------------------------------------------------------------- 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 560 VAL Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain B residue 1163 ASN Chi-restraints excluded: chain B residue 1335 GLU Chi-restraints excluded: chain B residue 1362 ASP Chi-restraints excluded: chain B residue 1505 LEU Chi-restraints excluded: chain C residue 188 ASN 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 82 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN A 606 ASN ** B1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN C 165 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 13304 Z= 0.390 Angle : 0.568 7.337 18022 Z= 0.302 Chirality : 0.045 0.264 2041 Planarity : 0.004 0.047 2324 Dihedral : 4.279 19.561 1782 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.02 % Allowed : 12.44 % Favored : 85.55 % 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: 2.01 (0.25), residues: 421 sheet: 0.70 (0.22), residues: 525 loop : 0.19 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 552 HIS 0.007 0.001 HIS C 282 PHE 0.017 0.002 PHE A 529 TYR 0.029 0.002 TYR B1432 ARG 0.004 0.000 ARG A 207 *********************** 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 478 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 449 time to evaluate : 2.261 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: 0.7421 (m-30) cc_final: 0.6938 (m-30) REVERT: A 65 LYS cc_start: 0.7761 (tppt) cc_final: 0.7234 (tptt) REVERT: A 82 HIS cc_start: 0.7210 (m-70) cc_final: 0.6828 (m170) REVERT: A 154 HIS cc_start: 0.7415 (p90) cc_final: 0.6948 (p90) REVERT: A 226 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7108 (mt-10) REVERT: A 240 GLU cc_start: 0.7456 (mt-10) cc_final: 0.6733 (pt0) REVERT: A 241 LYS cc_start: 0.8020 (ptpt) cc_final: 0.7701 (mttm) REVERT: A 248 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7272 (mm-30) REVERT: A 254 THR cc_start: 0.7816 (m) cc_final: 0.7484 (p) REVERT: A 258 ARG cc_start: 0.7384 (ptp-170) cc_final: 0.6982 (ptm160) REVERT: A 264 LYS cc_start: 0.7363 (mtmt) cc_final: 0.7052 (mtmm) REVERT: A 286 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7450 (mm-30) REVERT: A 295 ASP cc_start: 0.7397 (t0) cc_final: 0.6872 (t0) REVERT: A 299 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6976 (mt-10) REVERT: A 399 SER cc_start: 0.7907 (t) cc_final: 0.7315 (m) REVERT: A 435 GLU cc_start: 0.6669 (mt-10) cc_final: 0.6460 (mt-10) REVERT: A 451 ASN cc_start: 0.7167 (t0) cc_final: 0.6782 (t0) REVERT: A 488 ARG cc_start: 0.7442 (mtp180) cc_final: 0.7088 (mtp85) REVERT: A 505 ARG cc_start: 0.7816 (mtt180) cc_final: 0.7325 (mtt180) REVERT: A 641 ASP cc_start: 0.7619 (m-30) cc_final: 0.7355 (m-30) REVERT: B 769 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7113 (mt-10) REVERT: B 776 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6401 (mp0) REVERT: B 803 GLU cc_start: 0.7620 (tt0) cc_final: 0.7358 (tt0) REVERT: B 828 ASP cc_start: 0.7692 (m-30) cc_final: 0.7404 (m-30) REVERT: B 843 GLU cc_start: 0.7564 (tt0) cc_final: 0.6956 (tt0) REVERT: B 846 GLU cc_start: 0.7724 (tt0) cc_final: 0.7454 (tt0) REVERT: B 859 GLU cc_start: 0.7361 (tt0) cc_final: 0.7089 (tm-30) REVERT: B 904 LYS cc_start: 0.7890 (mtpp) cc_final: 0.7409 (mtpp) REVERT: B 931 VAL cc_start: 0.7420 (t) cc_final: 0.7201 (t) REVERT: B 933 PRO cc_start: 0.8275 (Cg_exo) cc_final: 0.7980 (Cg_endo) REVERT: B 960 GLU cc_start: 0.6383 (mm-30) cc_final: 0.5439 (mm-30) REVERT: B 977 GLU cc_start: 0.6788 (tt0) cc_final: 0.6232 (tt0) REVERT: B 992 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6849 (mm-30) REVERT: B 1033 GLN cc_start: 0.6201 (mm-40) cc_final: 0.5921 (mt0) REVERT: B 1061 GLN cc_start: 0.7057 (mt0) cc_final: 0.6761 (mt0) REVERT: B 1298 LEU cc_start: 0.6070 (mt) cc_final: 0.5853 (mt) REVERT: B 1348 TYR cc_start: 0.6736 (p90) cc_final: 0.6488 (p90) REVERT: B 1360 LYS cc_start: 0.6696 (mmtm) cc_final: 0.6347 (mmmm) REVERT: B 1362 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6736 (t0) REVERT: B 1364 LYS cc_start: 0.7257 (tttt) cc_final: 0.6763 (tppp) REVERT: B 1420 GLN cc_start: 0.6842 (tm-30) cc_final: 0.6468 (tm-30) REVERT: B 1423 ASN cc_start: 0.6907 (t0) cc_final: 0.6703 (t0) REVERT: B 1432 TYR cc_start: 0.7185 (t80) cc_final: 0.6960 (t80) REVERT: B 1478 LYS cc_start: 0.7300 (ttpt) cc_final: 0.6925 (tttt) REVERT: B 1487 GLU cc_start: 0.6887 (tt0) cc_final: 0.6431 (tt0) REVERT: B 1512 ARG cc_start: 0.5986 (mtp-110) cc_final: 0.4621 (mtt90) REVERT: B 1513 CYS cc_start: 0.6275 (t) cc_final: 0.6022 (t) REVERT: C 32 LYS cc_start: 0.7531 (pttm) cc_final: 0.7155 (pttm) REVERT: C 33 ASN cc_start: 0.7297 (m-40) cc_final: 0.6806 (m-40) REVERT: C 37 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7743 (mt-10) REVERT: C 106 VAL cc_start: 0.8114 (t) cc_final: 0.7720 (p) REVERT: C 107 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7556 (mmtt) REVERT: C 123 GLU cc_start: 0.7860 (tp30) cc_final: 0.7437 (tp30) REVERT: C 126 LYS cc_start: 0.8141 (tttt) cc_final: 0.7464 (tttt) REVERT: C 130 ASP cc_start: 0.7020 (m-30) cc_final: 0.6633 (m-30) REVERT: C 255 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7538 (mt-10) REVERT: C 263 GLU cc_start: 0.7787 (tp30) cc_final: 0.6990 (tp30) REVERT: C 267 LYS cc_start: 0.7798 (mmtp) cc_final: 0.7385 (mmtp) REVERT: C 269 LYS cc_start: 0.7784 (tppt) cc_final: 0.7547 (tppt) REVERT: C 272 GLU cc_start: 0.7668 (tt0) cc_final: 0.7244 (tt0) REVERT: C 276 GLU cc_start: 0.7451 (mt-10) cc_final: 0.6975 (mt-10) REVERT: C 277 LYS cc_start: 0.7493 (mttm) cc_final: 0.7275 (mttm) REVERT: C 288 TYR cc_start: 0.8075 (m-80) cc_final: 0.7760 (m-10) outliers start: 29 outliers final: 20 residues processed: 462 average time/residue: 0.7083 time to fit residues: 450.5500 Evaluate side-chains 462 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 441 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 1152 GLN Chi-restraints excluded: chain B residue 1163 ASN Chi-restraints excluded: chain B residue 1308 THR Chi-restraints excluded: chain B residue 1335 GLU Chi-restraints excluded: chain B residue 1345 VAL Chi-restraints excluded: chain B residue 1358 CYS 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 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 147 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 42 optimal weight: 0.0870 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 774 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13304 Z= 0.228 Angle : 0.538 13.354 18022 Z= 0.282 Chirality : 0.044 0.275 2041 Planarity : 0.004 0.039 2324 Dihedral : 4.138 18.376 1782 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.95 % Allowed : 13.90 % Favored : 84.16 % 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: 1.23 (0.21), residues: 1641 helix: 2.01 (0.26), residues: 424 sheet: 0.74 (0.22), residues: 532 loop : 0.23 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 223 HIS 0.007 0.001 HIS C 282 PHE 0.014 0.001 PHE A 529 TYR 0.017 0.001 TYR B1282 ARG 0.006 0.000 ARG A 207 *********************** 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 463 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 435 time to evaluate : 2.411 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: 0.7423 (m-30) cc_final: 0.6909 (m-30) REVERT: A 82 HIS cc_start: 0.7239 (m-70) cc_final: 0.6837 (m170) REVERT: A 118 GLU cc_start: 0.7635 (pt0) cc_final: 0.7370 (pt0) REVERT: A 154 HIS cc_start: 0.7397 (p90) cc_final: 0.6951 (p90) REVERT: A 226 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7076 (mt-10) REVERT: A 240 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6717 (pt0) REVERT: A 241 LYS cc_start: 0.8008 (ptpt) cc_final: 0.7658 (mttm) REVERT: A 248 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7198 (mm-30) REVERT: A 254 THR cc_start: 0.7798 (m) cc_final: 0.7413 (p) REVERT: A 258 ARG cc_start: 0.7364 (ptp-170) cc_final: 0.6987 (ptm160) REVERT: A 264 LYS cc_start: 0.7256 (mtmt) cc_final: 0.6966 (mtmm) REVERT: A 286 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7442 (mm-30) REVERT: A 295 ASP cc_start: 0.7364 (t0) cc_final: 0.6862 (t0) REVERT: A 299 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6965 (mt-10) REVERT: A 399 SER cc_start: 0.7851 (t) cc_final: 0.7234 (m) REVERT: A 435 GLU cc_start: 0.6648 (mt-10) cc_final: 0.6409 (mt-10) REVERT: A 451 ASN cc_start: 0.7162 (t0) cc_final: 0.6781 (t0) REVERT: A 488 ARG cc_start: 0.7357 (mtp180) cc_final: 0.7050 (mtp85) REVERT: A 505 ARG cc_start: 0.7671 (mtt180) cc_final: 0.7321 (mtt180) REVERT: A 641 ASP cc_start: 0.7600 (m-30) cc_final: 0.7322 (m-30) REVERT: B 776 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6457 (mp0) REVERT: B 803 GLU cc_start: 0.7598 (tt0) cc_final: 0.7322 (tt0) REVERT: B 822 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7025 (mt-10) REVERT: B 828 ASP cc_start: 0.7661 (m-30) cc_final: 0.7368 (m-30) REVERT: B 843 GLU cc_start: 0.7593 (tt0) cc_final: 0.6992 (tt0) REVERT: B 859 GLU cc_start: 0.7353 (tt0) cc_final: 0.7115 (tm-30) REVERT: B 904 LYS cc_start: 0.7881 (mtpp) cc_final: 0.7408 (mtpp) REVERT: B 931 VAL cc_start: 0.7425 (t) cc_final: 0.7195 (t) REVERT: B 933 PRO cc_start: 0.8278 (Cg_exo) cc_final: 0.7997 (Cg_endo) REVERT: B 975 GLU cc_start: 0.6431 (tp30) cc_final: 0.5952 (tp30) REVERT: B 977 GLU cc_start: 0.6785 (tt0) cc_final: 0.6190 (tt0) REVERT: B 992 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6728 (mm-30) REVERT: B 1033 GLN cc_start: 0.6168 (mm-40) cc_final: 0.5928 (mt0) REVERT: B 1061 GLN cc_start: 0.7027 (mt0) cc_final: 0.6745 (mt0) REVERT: B 1298 LEU cc_start: 0.6042 (mt) cc_final: 0.5835 (mt) REVERT: B 1310 ARG cc_start: 0.6947 (mtp-110) cc_final: 0.6558 (mtp-110) REVERT: B 1325 LYS cc_start: 0.7505 (mmmm) cc_final: 0.6967 (mmmm) REVERT: B 1348 TYR cc_start: 0.6773 (p90) cc_final: 0.6487 (p90) REVERT: B 1364 LYS cc_start: 0.7220 (tttt) cc_final: 0.6735 (tppp) REVERT: B 1420 GLN cc_start: 0.6848 (tm-30) cc_final: 0.6497 (tm-30) REVERT: B 1423 ASN cc_start: 0.6921 (t0) cc_final: 0.6711 (t0) REVERT: B 1432 TYR cc_start: 0.7245 (t80) cc_final: 0.6938 (t80) REVERT: B 1478 LYS cc_start: 0.7331 (ttpt) cc_final: 0.6940 (tttt) REVERT: B 1509 GLU cc_start: 0.6939 (tt0) cc_final: 0.6455 (tp30) REVERT: B 1512 ARG cc_start: 0.5956 (mtp-110) cc_final: 0.4600 (mtt90) REVERT: B 1513 CYS cc_start: 0.6281 (t) cc_final: 0.6055 (t) REVERT: C 32 LYS cc_start: 0.7471 (pttm) cc_final: 0.7160 (pttm) REVERT: C 37 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7732 (mt-10) REVERT: C 106 VAL cc_start: 0.8130 (t) cc_final: 0.7748 (p) REVERT: C 123 GLU cc_start: 0.7853 (tp30) cc_final: 0.7396 (tp30) REVERT: C 126 LYS cc_start: 0.8188 (tttt) cc_final: 0.7464 (tttt) REVERT: C 130 ASP cc_start: 0.7026 (m-30) cc_final: 0.6647 (m-30) REVERT: C 255 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7578 (mt-10) REVERT: C 263 GLU cc_start: 0.7825 (tp30) cc_final: 0.6928 (tp30) REVERT: C 267 LYS cc_start: 0.7799 (mmtp) cc_final: 0.7337 (mmtp) REVERT: C 269 LYS cc_start: 0.7787 (tppt) cc_final: 0.7548 (tppt) REVERT: C 272 GLU cc_start: 0.7652 (tt0) cc_final: 0.7184 (tt0) REVERT: C 276 GLU cc_start: 0.7446 (mt-10) cc_final: 0.6971 (mt-10) REVERT: C 277 LYS cc_start: 0.7517 (mttm) cc_final: 0.7304 (mttm) REVERT: C 288 TYR cc_start: 0.8085 (m-80) cc_final: 0.7820 (m-10) outliers start: 28 outliers final: 21 residues processed: 447 average time/residue: 0.7268 time to fit residues: 444.0486 Evaluate side-chains 445 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 424 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER 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 560 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1163 ASN Chi-restraints excluded: chain B residue 1345 VAL Chi-restraints excluded: chain B residue 1358 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 0.0170 chunk 135 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- 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** B1229 ASN B1281 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 13304 Z= 0.276 Angle : 0.536 13.098 18022 Z= 0.281 Chirality : 0.044 0.320 2041 Planarity : 0.004 0.036 2324 Dihedral : 4.135 19.134 1782 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.74 % Allowed : 14.73 % Favored : 83.53 % 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: 1.29 (0.21), residues: 1641 helix: 2.03 (0.26), residues: 423 sheet: 0.86 (0.22), residues: 521 loop : 0.22 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 166 HIS 0.007 0.001 HIS C 282 PHE 0.014 0.001 PHE A 529 TYR 0.025 0.002 TYR B1282 ARG 0.006 0.000 ARG A 207 *********************** 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 448 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 423 time to evaluate : 2.138 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: 0.7440 (m-30) cc_final: 0.6899 (m-30) REVERT: A 82 HIS cc_start: 0.7340 (m-70) cc_final: 0.6910 (m170) REVERT: A 118 GLU cc_start: 0.7617 (pt0) cc_final: 0.7297 (pt0) REVERT: A 154 HIS cc_start: 0.7391 (p90) cc_final: 0.6957 (p90) REVERT: A 226 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7086 (mt-10) REVERT: A 240 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6719 (pt0) REVERT: A 241 LYS cc_start: 0.8001 (ptpt) cc_final: 0.7670 (mttm) REVERT: A 248 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7209 (mm-30) REVERT: A 258 ARG cc_start: 0.7310 (ptp-170) cc_final: 0.6950 (ptm160) REVERT: A 264 LYS cc_start: 0.7246 (mtmt) cc_final: 0.6972 (mtmm) REVERT: A 286 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 295 ASP cc_start: 0.7363 (t0) cc_final: 0.6886 (t0) REVERT: A 299 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6964 (mt-10) REVERT: A 399 SER cc_start: 0.7800 (t) cc_final: 0.7213 (m) REVERT: A 435 GLU cc_start: 0.6662 (mt-10) cc_final: 0.6411 (mt-10) REVERT: A 451 ASN cc_start: 0.7187 (t0) cc_final: 0.6828 (t0) REVERT: A 478 ARG cc_start: 0.7332 (ttt90) cc_final: 0.7027 (ttt90) REVERT: A 488 ARG cc_start: 0.7394 (mtp180) cc_final: 0.7054 (mtp85) REVERT: A 505 ARG cc_start: 0.7698 (mtt180) cc_final: 0.7368 (mtt180) REVERT: A 641 ASP cc_start: 0.7624 (m-30) cc_final: 0.7340 (m-30) REVERT: B 769 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7208 (mt-10) REVERT: B 776 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6433 (mp0) REVERT: B 803 GLU cc_start: 0.7606 (tt0) cc_final: 0.7368 (tt0) REVERT: B 822 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7068 (mt-10) REVERT: B 828 ASP cc_start: 0.7631 (m-30) cc_final: 0.7331 (m-30) REVERT: B 843 GLU cc_start: 0.7571 (tt0) cc_final: 0.6967 (tt0) REVERT: B 904 LYS cc_start: 0.7923 (mtpp) cc_final: 0.7508 (mtpp) REVERT: B 933 PRO cc_start: 0.8279 (Cg_exo) cc_final: 0.7993 (Cg_endo) REVERT: B 977 GLU cc_start: 0.6775 (tt0) cc_final: 0.6135 (tt0) REVERT: B 992 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6915 (mm-30) REVERT: B 1061 GLN cc_start: 0.7108 (mt0) cc_final: 0.6860 (mt0) REVERT: B 1310 ARG cc_start: 0.6905 (mtp-110) cc_final: 0.6636 (mtp-110) REVERT: B 1335 GLU cc_start: 0.5868 (mt-10) cc_final: 0.5433 (mt-10) REVERT: B 1348 TYR cc_start: 0.6812 (p90) cc_final: 0.6444 (p90) REVERT: B 1362 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6772 (t0) REVERT: B 1364 LYS cc_start: 0.7238 (tttt) cc_final: 0.6759 (tppp) REVERT: B 1420 GLN cc_start: 0.6842 (tm-30) cc_final: 0.6491 (tm-30) REVERT: B 1423 ASN cc_start: 0.6933 (t0) cc_final: 0.6721 (t0) REVERT: B 1432 TYR cc_start: 0.7247 (t80) cc_final: 0.6943 (t80) REVERT: B 1478 LYS cc_start: 0.7316 (ttpt) cc_final: 0.6927 (tttt) REVERT: B 1509 GLU cc_start: 0.6973 (tt0) cc_final: 0.6491 (tp30) REVERT: B 1513 CYS cc_start: 0.6258 (t) cc_final: 0.6046 (t) REVERT: C 32 LYS cc_start: 0.7464 (pttm) cc_final: 0.7148 (pttm) REVERT: C 37 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7747 (mt-10) REVERT: C 83 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7467 (tm-30) REVERT: C 106 VAL cc_start: 0.8198 (t) cc_final: 0.7825 (p) REVERT: C 123 GLU cc_start: 0.7848 (tp30) cc_final: 0.7422 (tp30) REVERT: C 126 LYS cc_start: 0.8206 (tttt) cc_final: 0.7468 (tttt) REVERT: C 130 ASP cc_start: 0.7040 (m-30) cc_final: 0.6648 (m-30) REVERT: C 211 TRP cc_start: 0.8247 (m-10) cc_final: 0.8045 (m-10) REVERT: C 255 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7557 (mt-10) REVERT: C 263 GLU cc_start: 0.7900 (tp30) cc_final: 0.6957 (tp30) REVERT: C 269 LYS cc_start: 0.7779 (tppt) cc_final: 0.7491 (tppp) REVERT: C 272 GLU cc_start: 0.7610 (tt0) cc_final: 0.7147 (tt0) REVERT: C 276 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6961 (mt-10) REVERT: C 288 TYR cc_start: 0.8159 (m-80) cc_final: 0.7823 (m-10) outliers start: 25 outliers final: 20 residues processed: 436 average time/residue: 0.7429 time to fit residues: 448.6099 Evaluate side-chains 437 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 416 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER 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 327 SER Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain B residue 1163 ASN Chi-restraints excluded: chain B residue 1345 VAL Chi-restraints excluded: chain B residue 1358 CYS Chi-restraints excluded: chain B residue 1362 ASP Chi-restraints excluded: chain B residue 1383 THR Chi-restraints excluded: chain B residue 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 212 SER 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 53 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.141 13304 Z= 0.444 Angle : 0.585 12.517 18022 Z= 0.309 Chirality : 0.046 0.387 2041 Planarity : 0.004 0.041 2324 Dihedral : 4.342 18.683 1782 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.64 % Allowed : 14.18 % Favored : 83.18 % 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: 1.00 (0.20), residues: 1641 helix: 1.78 (0.25), residues: 421 sheet: 0.80 (0.22), residues: 515 loop : -0.03 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 166 HIS 0.007 0.001 HIS C 282 PHE 0.019 0.002 PHE A 529 TYR 0.021 0.002 TYR B1282 ARG 0.008 0.000 ARG A 207 *********************** 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 471 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 433 time to evaluate : 2.085 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: 0.7517 (OUTLIER) cc_final: 0.6970 (m-30) REVERT: A 82 HIS cc_start: 0.7404 (m-70) cc_final: 0.7065 (m90) REVERT: A 118 GLU cc_start: 0.7651 (pt0) cc_final: 0.7277 (pt0) REVERT: A 154 HIS cc_start: 0.7427 (p90) cc_final: 0.6985 (p90) REVERT: A 226 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7066 (mt-10) REVERT: A 240 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6724 (pt0) REVERT: A 241 LYS cc_start: 0.8034 (ptpt) cc_final: 0.7733 (mttm) REVERT: A 248 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7220 (mm-30) REVERT: A 258 ARG cc_start: 0.7301 (ptp-170) cc_final: 0.6931 (ptm160) REVERT: A 286 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7440 (mm-30) REVERT: A 295 ASP cc_start: 0.7420 (t0) cc_final: 0.6942 (t0) REVERT: A 299 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7022 (mt-10) REVERT: A 342 GLU cc_start: 0.7524 (mt-10) cc_final: 0.6992 (tt0) REVERT: A 387 VAL cc_start: 0.7992 (OUTLIER) cc_final: 0.7679 (m) REVERT: A 399 SER cc_start: 0.7771 (t) cc_final: 0.7209 (m) REVERT: A 412 ASN cc_start: 0.7945 (m110) cc_final: 0.7653 (t0) REVERT: A 435 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6553 (mt-10) REVERT: A 447 SER cc_start: 0.7782 (t) cc_final: 0.7340 (m) REVERT: A 451 ASN cc_start: 0.7246 (t0) cc_final: 0.6901 (t0) REVERT: A 488 ARG cc_start: 0.7485 (mtp180) cc_final: 0.7127 (mtp85) REVERT: A 502 LYS cc_start: 0.8085 (tttt) cc_final: 0.7860 (tttp) REVERT: A 505 ARG cc_start: 0.7756 (mtt180) cc_final: 0.7412 (mtt180) REVERT: A 641 ASP cc_start: 0.7653 (m-30) cc_final: 0.7401 (m-30) REVERT: B 776 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6681 (mm-30) REVERT: B 803 GLU cc_start: 0.7626 (tt0) cc_final: 0.7407 (tt0) REVERT: B 822 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7083 (mt-10) REVERT: B 843 GLU cc_start: 0.7570 (tt0) cc_final: 0.6952 (tt0) REVERT: B 904 LYS cc_start: 0.7884 (mtpp) cc_final: 0.7457 (mtpp) REVERT: B 933 PRO cc_start: 0.8282 (Cg_exo) cc_final: 0.8004 (Cg_endo) REVERT: B 975 GLU cc_start: 0.6610 (tp30) cc_final: 0.6039 (tp30) REVERT: B 992 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6893 (mm-30) REVERT: B 1061 GLN cc_start: 0.7198 (mt0) cc_final: 0.6971 (mt0) REVERT: B 1177 GLU cc_start: 0.6386 (mt-10) cc_final: 0.6118 (mt-10) REVERT: B 1323 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6379 (mt-10) REVERT: B 1325 LYS cc_start: 0.7532 (mmmm) cc_final: 0.6976 (mmmm) REVERT: B 1347 MET cc_start: 0.7235 (mtm) cc_final: 0.6586 (mtm) REVERT: B 1362 ASP cc_start: 0.7181 (OUTLIER) cc_final: 0.6693 (t0) REVERT: B 1364 LYS cc_start: 0.7305 (tttt) cc_final: 0.6790 (tppp) REVERT: B 1420 GLN cc_start: 0.6864 (tm-30) cc_final: 0.6494 (tm-30) REVERT: B 1432 TYR cc_start: 0.7246 (t80) cc_final: 0.6944 (t80) REVERT: B 1478 LYS cc_start: 0.7300 (ttpt) cc_final: 0.6926 (tttt) REVERT: B 1487 GLU cc_start: 0.6825 (tt0) cc_final: 0.6420 (tt0) REVERT: B 1513 CYS cc_start: 0.6281 (t) cc_final: 0.6055 (t) REVERT: C 32 LYS cc_start: 0.7543 (pttm) cc_final: 0.7213 (pttm) REVERT: C 37 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7787 (mt-10) REVERT: C 83 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7477 (tm-30) REVERT: C 103 ILE cc_start: 0.7943 (mm) cc_final: 0.7658 (mm) REVERT: C 106 VAL cc_start: 0.8253 (t) cc_final: 0.7880 (p) REVERT: C 107 LYS cc_start: 0.8151 (mmtt) cc_final: 0.7565 (mmtt) REVERT: C 123 GLU cc_start: 0.7906 (tp30) cc_final: 0.7650 (tp30) REVERT: C 126 LYS cc_start: 0.8229 (tttt) cc_final: 0.7504 (tttt) REVERT: C 130 ASP cc_start: 0.7101 (m-30) cc_final: 0.6710 (m-30) REVERT: C 211 TRP cc_start: 0.8259 (m-10) cc_final: 0.7993 (m-10) REVERT: C 263 GLU cc_start: 0.7916 (tp30) cc_final: 0.6954 (tp30) REVERT: C 269 LYS cc_start: 0.7787 (tppt) cc_final: 0.7483 (tppp) REVERT: C 272 GLU cc_start: 0.7669 (tt0) cc_final: 0.7200 (tt0) REVERT: C 276 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6990 (mt-10) REVERT: C 288 TYR cc_start: 0.8192 (m-80) cc_final: 0.7850 (m-10) outliers start: 38 outliers final: 26 residues processed: 450 average time/residue: 0.7401 time to fit residues: 461.1417 Evaluate side-chains 455 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 426 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 107 THR 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 387 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain B residue 1152 GLN Chi-restraints excluded: chain B residue 1163 ASN Chi-restraints excluded: chain B residue 1308 THR 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 1453 HIS Chi-restraints excluded: chain B residue 1505 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 212 SER 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 152 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 90 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 GLN A 606 ASN ** B1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1229 ASN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.185 13304 Z= 0.266 Angle : 0.556 13.797 18022 Z= 0.289 Chirality : 0.045 0.402 2041 Planarity : 0.004 0.036 2324 Dihedral : 4.188 18.749 1782 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.08 % Allowed : 15.77 % Favored : 82.14 % 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: 1.15 (0.21), residues: 1641 helix: 1.92 (0.25), residues: 421 sheet: 0.88 (0.22), residues: 515 loop : 0.05 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 211 HIS 0.005 0.001 HIS C 282 PHE 0.014 0.001 PHE A 529 TYR 0.018 0.001 TYR B1282 ARG 0.007 0.000 ARG A 207 *********************** 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 fitting. rotamer outliers: 30 poor density : 430 time to evaluate : 2.146 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: 0.7496 (OUTLIER) cc_final: 0.6964 (m-30) REVERT: A 82 HIS cc_start: 0.7398 (m-70) cc_final: 0.7053 (m90) REVERT: A 118 GLU cc_start: 0.7588 (pt0) cc_final: 0.7197 (pt0) REVERT: A 154 HIS cc_start: 0.7446 (p90) cc_final: 0.6983 (p90) REVERT: A 226 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7062 (mt-10) REVERT: A 237 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7211 (mm-30) REVERT: A 240 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6728 (pt0) REVERT: A 241 LYS cc_start: 0.8039 (ptpt) cc_final: 0.7728 (mttm) REVERT: A 248 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7215 (mm-30) REVERT: A 258 ARG cc_start: 0.7246 (ptp-170) cc_final: 0.6924 (ptm160) REVERT: A 286 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7369 (mm-30) REVERT: A 295 ASP cc_start: 0.7320 (t0) cc_final: 0.6934 (t0) REVERT: A 299 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7022 (mt-10) REVERT: A 342 GLU cc_start: 0.7549 (mt-10) cc_final: 0.6991 (tt0) REVERT: A 387 VAL cc_start: 0.8015 (OUTLIER) cc_final: 0.7703 (m) REVERT: A 399 SER cc_start: 0.7783 (t) cc_final: 0.7200 (m) REVERT: A 412 ASN cc_start: 0.7973 (m110) cc_final: 0.7683 (t0) REVERT: A 435 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6535 (mt-10) REVERT: A 451 ASN cc_start: 0.7268 (t0) cc_final: 0.6927 (t0) REVERT: A 488 ARG cc_start: 0.7443 (mtp180) cc_final: 0.7122 (mtp85) REVERT: A 502 LYS cc_start: 0.7986 (tttt) cc_final: 0.7643 (tttm) REVERT: A 505 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7399 (mtt180) REVERT: A 641 ASP cc_start: 0.7673 (m-30) cc_final: 0.7418 (m-30) REVERT: B 776 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6491 (mp0) REVERT: B 803 GLU cc_start: 0.7603 (tt0) cc_final: 0.7371 (tt0) REVERT: B 828 ASP cc_start: 0.7602 (m-30) cc_final: 0.7313 (m-30) REVERT: B 843 GLU cc_start: 0.7580 (tt0) cc_final: 0.6967 (tt0) REVERT: B 904 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7475 (mtpp) REVERT: B 933 PRO cc_start: 0.8279 (Cg_exo) cc_final: 0.8009 (Cg_endo) REVERT: B 982 LEU cc_start: 0.7218 (mm) cc_final: 0.6958 (mp) REVERT: B 992 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6890 (mm-30) REVERT: B 1061 GLN cc_start: 0.7145 (mt0) cc_final: 0.6919 (mt0) REVERT: B 1177 GLU cc_start: 0.6374 (mt-10) cc_final: 0.6120 (mt-10) REVERT: B 1364 LYS cc_start: 0.7272 (tttt) cc_final: 0.6780 (tppp) REVERT: B 1420 GLN cc_start: 0.6845 (tm-30) cc_final: 0.6522 (tm-30) REVERT: B 1432 TYR cc_start: 0.7248 (t80) cc_final: 0.6943 (t80) REVERT: B 1478 LYS cc_start: 0.7304 (ttpt) cc_final: 0.6940 (tttt) REVERT: B 1487 GLU cc_start: 0.6873 (tt0) cc_final: 0.6452 (tt0) REVERT: C 32 LYS cc_start: 0.7505 (pttm) cc_final: 0.7180 (pttm) REVERT: C 37 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7781 (mt-10) REVERT: C 83 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7448 (tm-30) REVERT: C 103 ILE cc_start: 0.7903 (mm) cc_final: 0.7612 (mm) REVERT: C 106 VAL cc_start: 0.8226 (t) cc_final: 0.7835 (p) REVERT: C 107 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7544 (mmtt) REVERT: C 123 GLU cc_start: 0.7858 (tp30) cc_final: 0.7597 (tp30) REVERT: C 126 LYS cc_start: 0.8222 (tttt) cc_final: 0.7477 (tttt) REVERT: C 130 ASP cc_start: 0.7101 (m-30) cc_final: 0.6680 (m-30) REVERT: C 211 TRP cc_start: 0.8156 (m-10) cc_final: 0.7554 (m-10) REVERT: C 263 GLU cc_start: 0.7898 (tp30) cc_final: 0.6905 (tp30) REVERT: C 269 LYS cc_start: 0.7793 (tppt) cc_final: 0.7501 (tppt) REVERT: C 272 GLU cc_start: 0.7618 (tt0) cc_final: 0.7126 (tt0) REVERT: C 276 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6920 (mt-10) REVERT: C 288 TYR cc_start: 0.8196 (m-80) cc_final: 0.7849 (m-10) outliers start: 30 outliers final: 24 residues processed: 442 average time/residue: 0.7072 time to fit residues: 428.6995 Evaluate side-chains 453 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 427 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 52 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 277 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain B residue 1163 ASN Chi-restraints excluded: chain B residue 1308 THR Chi-restraints excluded: chain B residue 1345 VAL 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 35 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 286 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 GLN A 606 ASN ** B1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1229 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 13304 Z= 0.287 Angle : 0.568 12.403 18022 Z= 0.292 Chirality : 0.044 0.351 2041 Planarity : 0.004 0.035 2324 Dihedral : 4.181 18.149 1782 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.43 % Allowed : 15.71 % Favored : 81.86 % 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: 1.17 (0.21), residues: 1641 helix: 1.90 (0.25), residues: 421 sheet: 0.91 (0.22), residues: 519 loop : 0.07 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 166 HIS 0.005 0.001 HIS C 282 PHE 0.015 0.001 PHE A 529 TYR 0.017 0.002 TYR B1282 ARG 0.004 0.000 ARG A 207 *********************** 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 468 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 433 time to evaluate : 2.108 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 37 GLU cc_start: 0.7156 (tp30) cc_final: 0.6832 (tp30) REVERT: A 52 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.6962 (m-30) REVERT: A 82 HIS cc_start: 0.7399 (m-70) cc_final: 0.7046 (m90) REVERT: A 118 GLU cc_start: 0.7545 (pt0) cc_final: 0.7145 (pt0) REVERT: A 154 HIS cc_start: 0.7433 (p90) cc_final: 0.6989 (p90) REVERT: A 226 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7066 (mt-10) REVERT: A 237 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7265 (mm-30) REVERT: A 240 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6734 (pt0) REVERT: A 241 LYS cc_start: 0.8049 (ptpt) cc_final: 0.7733 (mttm) REVERT: A 248 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7210 (mm-30) REVERT: A 258 ARG cc_start: 0.7257 (ptp-170) cc_final: 0.6932 (ptm160) REVERT: A 286 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7372 (mm-30) REVERT: A 299 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7013 (mt-10) REVERT: A 342 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7033 (tt0) REVERT: A 387 VAL cc_start: 0.8009 (OUTLIER) cc_final: 0.7697 (m) REVERT: A 399 SER cc_start: 0.7769 (t) cc_final: 0.7190 (m) REVERT: A 412 ASN cc_start: 0.7973 (m110) cc_final: 0.7672 (t0) REVERT: A 435 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6539 (mt-10) REVERT: A 451 ASN cc_start: 0.7280 (t0) cc_final: 0.6919 (t0) REVERT: A 488 ARG cc_start: 0.7458 (mtp180) cc_final: 0.7141 (mtp85) REVERT: A 502 LYS cc_start: 0.7988 (tttt) cc_final: 0.7600 (tttm) REVERT: A 505 ARG cc_start: 0.7711 (mtt180) cc_final: 0.7383 (mtt180) REVERT: A 641 ASP cc_start: 0.7677 (m-30) cc_final: 0.7423 (m-30) REVERT: B 776 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6504 (mp0) REVERT: B 843 GLU cc_start: 0.7583 (tt0) cc_final: 0.6980 (tt0) REVERT: B 904 LYS cc_start: 0.7912 (mtpp) cc_final: 0.7471 (mtpp) REVERT: B 933 PRO cc_start: 0.8278 (Cg_exo) cc_final: 0.8006 (Cg_endo) REVERT: B 982 LEU cc_start: 0.7213 (mm) cc_final: 0.6962 (mp) REVERT: B 992 GLU cc_start: 0.7462 (mm-30) cc_final: 0.6917 (mm-30) REVERT: B 1061 GLN cc_start: 0.7186 (mt0) cc_final: 0.6973 (mt0) REVERT: B 1177 GLU cc_start: 0.6370 (mt-10) cc_final: 0.6108 (mt-10) REVERT: B 1362 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6690 (t0) REVERT: B 1364 LYS cc_start: 0.7261 (tttt) cc_final: 0.6765 (tppp) REVERT: B 1420 GLN cc_start: 0.6850 (tm-30) cc_final: 0.6526 (tm-30) REVERT: B 1432 TYR cc_start: 0.7243 (t80) cc_final: 0.6928 (t80) REVERT: B 1478 LYS cc_start: 0.7307 (ttpt) cc_final: 0.6946 (tttt) REVERT: B 1487 GLU cc_start: 0.6913 (tt0) cc_final: 0.6445 (tt0) REVERT: C 32 LYS cc_start: 0.7494 (pttm) cc_final: 0.7171 (pttm) REVERT: C 37 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7794 (mt-10) REVERT: C 83 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7453 (tm-30) REVERT: C 103 ILE cc_start: 0.7917 (mm) cc_final: 0.7626 (mm) REVERT: C 106 VAL cc_start: 0.8251 (t) cc_final: 0.7878 (p) REVERT: C 107 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7547 (mmtt) REVERT: C 123 GLU cc_start: 0.7860 (tp30) cc_final: 0.7598 (tp30) REVERT: C 126 LYS cc_start: 0.8226 (tttt) cc_final: 0.7500 (tttt) REVERT: C 130 ASP cc_start: 0.7105 (m-30) cc_final: 0.6717 (m-30) REVERT: C 211 TRP cc_start: 0.8188 (m-10) cc_final: 0.7597 (m-10) REVERT: C 263 GLU cc_start: 0.7937 (tp30) cc_final: 0.6966 (tp30) REVERT: C 269 LYS cc_start: 0.7723 (tppt) cc_final: 0.7437 (tppt) REVERT: C 272 GLU cc_start: 0.7661 (tt0) cc_final: 0.7152 (tt0) REVERT: C 276 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6919 (mt-10) REVERT: C 288 TYR cc_start: 0.8211 (m-80) cc_final: 0.7852 (m-10) outliers start: 35 outliers final: 25 residues processed: 450 average time/residue: 0.7248 time to fit residues: 451.1403 Evaluate side-chains 457 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 429 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 52 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 277 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain B residue 1163 ASN Chi-restraints excluded: chain B residue 1308 THR 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 35 THR 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 212 SER Chi-restraints excluded: chain C residue 286 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 138 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 88 optimal weight: 0.0770 chunk 64 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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** B1229 ASN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 13304 Z= 0.242 Angle : 0.553 12.332 18022 Z= 0.284 Chirality : 0.044 0.378 2041 Planarity : 0.004 0.035 2324 Dihedral : 4.140 18.479 1782 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.22 % Allowed : 15.91 % Favored : 81.86 % 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: 1.23 (0.21), residues: 1641 helix: 1.94 (0.25), residues: 423 sheet: 0.92 (0.22), residues: 519 loop : 0.12 (0.24), residues: 699 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 0.013 0.001 PHE A 529 TYR 0.017 0.001 TYR B1282 ARG 0.005 0.000 ARG B1512 *********************** 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 464 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 432 time to evaluate : 2.132 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: 0.7489 (OUTLIER) cc_final: 0.6947 (m-30) REVERT: A 82 HIS cc_start: 0.7400 (m-70) cc_final: 0.7039 (m90) REVERT: A 118 GLU cc_start: 0.7547 (pt0) cc_final: 0.7132 (pt0) REVERT: A 226 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7054 (mt-10) REVERT: A 237 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7315 (mm-30) REVERT: A 240 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6768 (pt0) REVERT: A 241 LYS cc_start: 0.8049 (ptpt) cc_final: 0.7726 (mttm) REVERT: A 248 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7210 (mm-30) REVERT: A 258 ARG cc_start: 0.7245 (ptp-170) cc_final: 0.6925 (ptm160) REVERT: A 286 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7346 (mm-30) REVERT: A 295 ASP cc_start: 0.7363 (t0) cc_final: 0.7050 (t0) REVERT: A 299 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7032 (mt-10) REVERT: A 342 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7050 (tt0) REVERT: A 387 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7757 (m) REVERT: A 399 SER cc_start: 0.7809 (t) cc_final: 0.7220 (m) REVERT: A 412 ASN cc_start: 0.7973 (m110) cc_final: 0.7674 (t0) REVERT: A 435 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6508 (mt-10) REVERT: A 451 ASN cc_start: 0.7272 (t0) cc_final: 0.6915 (t0) REVERT: A 488 ARG cc_start: 0.7427 (mtp180) cc_final: 0.7118 (mtp85) REVERT: A 502 LYS cc_start: 0.7962 (tttt) cc_final: 0.7611 (tttm) REVERT: A 505 ARG cc_start: 0.7677 (mtt180) cc_final: 0.7353 (mtt180) REVERT: A 641 ASP cc_start: 0.7669 (m-30) cc_final: 0.7417 (m-30) REVERT: B 776 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6508 (mp0) REVERT: B 843 GLU cc_start: 0.7579 (tt0) cc_final: 0.6973 (tt0) REVERT: B 904 LYS cc_start: 0.7899 (mtpp) cc_final: 0.7457 (mtpp) REVERT: B 933 PRO cc_start: 0.8270 (Cg_exo) cc_final: 0.7999 (Cg_endo) REVERT: B 982 LEU cc_start: 0.7205 (mm) cc_final: 0.6957 (mp) REVERT: B 992 GLU cc_start: 0.7476 (mm-30) cc_final: 0.6953 (mm-30) REVERT: B 1061 GLN cc_start: 0.7147 (mt0) cc_final: 0.6936 (mt0) REVERT: B 1096 ASP cc_start: 0.6893 (m-30) cc_final: 0.6687 (t70) REVERT: B 1177 GLU cc_start: 0.6398 (mt-10) cc_final: 0.6136 (mt-10) REVERT: B 1333 THR cc_start: 0.6422 (m) cc_final: 0.5938 (p) REVERT: B 1362 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.6731 (t0) REVERT: B 1364 LYS cc_start: 0.7251 (tttt) cc_final: 0.6743 (tppp) REVERT: B 1420 GLN cc_start: 0.6851 (tm-30) cc_final: 0.6524 (tm-30) REVERT: B 1432 TYR cc_start: 0.7243 (t80) cc_final: 0.6921 (t80) REVERT: B 1478 LYS cc_start: 0.7324 (ttpt) cc_final: 0.6955 (tttt) REVERT: B 1487 GLU cc_start: 0.6922 (tt0) cc_final: 0.6444 (tt0) REVERT: B 1509 GLU cc_start: 0.7003 (tt0) cc_final: 0.6480 (tp30) REVERT: C 32 LYS cc_start: 0.7472 (pttm) cc_final: 0.7154 (pttm) REVERT: C 37 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7791 (mt-10) REVERT: C 83 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7461 (tm-30) REVERT: C 106 VAL cc_start: 0.8227 (t) cc_final: 0.7833 (p) REVERT: C 107 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7541 (mmtt) REVERT: C 123 GLU cc_start: 0.7850 (tp30) cc_final: 0.7600 (tp30) REVERT: C 126 LYS cc_start: 0.8215 (tttt) cc_final: 0.7461 (tttt) REVERT: C 130 ASP cc_start: 0.7105 (m-30) cc_final: 0.6680 (m-30) REVERT: C 211 TRP cc_start: 0.8173 (m-10) cc_final: 0.7597 (m-10) REVERT: C 263 GLU cc_start: 0.7913 (tp30) cc_final: 0.6920 (tp30) REVERT: C 269 LYS cc_start: 0.7741 (tppt) cc_final: 0.7475 (tppt) REVERT: C 272 GLU cc_start: 0.7632 (tt0) cc_final: 0.7138 (tt0) REVERT: C 276 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6920 (mt-10) REVERT: C 288 TYR cc_start: 0.8172 (m-80) cc_final: 0.7811 (m-10) outliers start: 32 outliers final: 26 residues processed: 446 average time/residue: 0.7174 time to fit residues: 437.3735 Evaluate side-chains 457 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 428 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 52 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 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 612 THR Chi-restraints excluded: chain B residue 1163 ASN Chi-restraints excluded: chain B residue 1308 THR 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 35 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 212 SER 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 96 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 100 optimal weight: 0.0670 chunk 79 optimal weight: 0.7980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 13304 Z= 0.258 Angle : 0.555 12.090 18022 Z= 0.284 Chirality : 0.044 0.352 2041 Planarity : 0.004 0.035 2324 Dihedral : 4.109 19.173 1782 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.95 % Allowed : 16.33 % Favored : 81.72 % 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: 1.22 (0.21), residues: 1641 helix: 1.99 (0.26), residues: 421 sheet: 0.91 (0.22), residues: 517 loop : 0.09 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 166 HIS 0.004 0.001 HIS C 282 PHE 0.013 0.001 PHE A 529 TYR 0.014 0.001 TYR B1282 ARG 0.011 0.000 ARG A 207 ********************** 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 459 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 431 time to evaluate : 2.132 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: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.6951 (m-30) REVERT: A 82 HIS cc_start: 0.7385 (m-70) cc_final: 0.7020 (m90) REVERT: A 118 GLU cc_start: 0.7513 (pt0) cc_final: 0.7074 (pt0) REVERT: A 154 HIS cc_start: 0.7380 (p90) cc_final: 0.7099 (p90) REVERT: A 168 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6828 (mt-10) REVERT: A 226 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7052 (mt-10) REVERT: A 240 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6757 (pt0) REVERT: A 248 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7215 (mm-30) REVERT: A 258 ARG cc_start: 0.7243 (ptp-170) cc_final: 0.6930 (ptm160) REVERT: A 286 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7345 (mm-30) REVERT: A 299 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7025 (mt-10) REVERT: A 342 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7078 (tt0) REVERT: A 387 VAL cc_start: 0.8088 (OUTLIER) cc_final: 0.7769 (m) REVERT: A 399 SER cc_start: 0.7800 (t) cc_final: 0.7217 (m) REVERT: A 435 GLU cc_start: 0.6733 (mt-10) cc_final: 0.6494 (mt-10) REVERT: A 451 ASN cc_start: 0.7285 (t0) cc_final: 0.6932 (t0) REVERT: A 488 ARG cc_start: 0.7422 (mtp180) cc_final: 0.7095 (mtp85) REVERT: A 502 LYS cc_start: 0.7951 (tttt) cc_final: 0.7730 (tttp) REVERT: A 505 ARG cc_start: 0.7651 (mtt180) cc_final: 0.7375 (mtt180) REVERT: A 641 ASP cc_start: 0.7669 (m-30) cc_final: 0.7427 (m-30) REVERT: B 776 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6572 (mm-30) REVERT: B 843 GLU cc_start: 0.7543 (tt0) cc_final: 0.6960 (tt0) REVERT: B 904 LYS cc_start: 0.7900 (mtpp) cc_final: 0.7465 (mtpp) REVERT: B 933 PRO cc_start: 0.8263 (Cg_exo) cc_final: 0.7990 (Cg_endo) REVERT: B 982 LEU cc_start: 0.7201 (mm) cc_final: 0.6969 (mp) REVERT: B 992 GLU cc_start: 0.7497 (mm-30) cc_final: 0.6959 (mm-30) REVERT: B 1270 GLN cc_start: 0.6458 (mm-40) cc_final: 0.6038 (mm-40) REVERT: B 1333 THR cc_start: 0.6438 (m) cc_final: 0.5944 (p) REVERT: B 1362 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6724 (t0) REVERT: B 1364 LYS cc_start: 0.7256 (tttt) cc_final: 0.6742 (tppp) REVERT: B 1420 GLN cc_start: 0.6850 (tm-30) cc_final: 0.6522 (tm-30) REVERT: B 1432 TYR cc_start: 0.7232 (t80) cc_final: 0.6919 (t80) REVERT: B 1449 ASP cc_start: 0.7408 (m-30) cc_final: 0.7174 (m-30) REVERT: B 1478 LYS cc_start: 0.7329 (ttpt) cc_final: 0.6960 (tttt) REVERT: C 32 LYS cc_start: 0.7451 (pttm) cc_final: 0.7142 (pttm) REVERT: C 37 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7795 (mt-10) REVERT: C 83 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7453 (tm-30) REVERT: C 106 VAL cc_start: 0.8250 (t) cc_final: 0.7860 (p) REVERT: C 107 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7558 (mmtt) REVERT: C 123 GLU cc_start: 0.7851 (tp30) cc_final: 0.7599 (tp30) REVERT: C 126 LYS cc_start: 0.8211 (tttt) cc_final: 0.7471 (tttt) REVERT: C 130 ASP cc_start: 0.7104 (m-30) cc_final: 0.6722 (m-30) REVERT: C 211 TRP cc_start: 0.8190 (m-10) cc_final: 0.7605 (m-10) REVERT: C 269 LYS cc_start: 0.7759 (tppt) cc_final: 0.7451 (tppt) REVERT: C 272 GLU cc_start: 0.7655 (tt0) cc_final: 0.7152 (tt0) REVERT: C 276 GLU cc_start: 0.7418 (mt-10) cc_final: 0.6930 (mt-10) REVERT: C 288 TYR cc_start: 0.8161 (m-80) cc_final: 0.7852 (m-10) outliers start: 28 outliers final: 22 residues processed: 444 average time/residue: 0.7109 time to fit residues: 432.6950 Evaluate side-chains 449 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 424 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 52 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 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 612 THR Chi-restraints excluded: chain B residue 1163 ASN Chi-restraints excluded: chain B residue 1362 ASP Chi-restraints excluded: chain B residue 1366 THR Chi-restraints excluded: chain B residue 1383 THR Chi-restraints excluded: chain B residue 1453 HIS Chi-restraints excluded: chain B residue 1505 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 212 SER 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 103 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 119 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1242 GLN ** 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 = 0.3352 r_free = 0.3352 target = 0.107924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.093907 restraints weight = 60367.373| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.28 r_work: 0.3018 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 13304 Z= 0.304 Angle : 0.561 11.919 18022 Z= 0.289 Chirality : 0.044 0.344 2041 Planarity : 0.004 0.036 2324 Dihedral : 4.159 19.635 1782 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.02 % Allowed : 16.68 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.89 (0.26), residues: 421 sheet: 0.87 (0.22), residues: 517 loop : 0.02 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 166 HIS 0.004 0.001 HIS A 457 PHE 0.015 0.001 PHE A 529 TYR 0.015 0.002 TYR B1282 ARG 0.008 0.000 ARG A 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8934.43 seconds wall clock time: 158 minutes 58.59 seconds (9538.59 seconds total)