Starting phenix.real_space_refine on Thu Feb 15 12:37:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bm0_7114/02_2024/6bm0_7114.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bm0_7114/02_2024/6bm0_7114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bm0_7114/02_2024/6bm0_7114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bm0_7114/02_2024/6bm0_7114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bm0_7114/02_2024/6bm0_7114.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bm0_7114/02_2024/6bm0_7114.pdb" } resolution = 3.8 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= -0.000 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 7841 2.51 5 N 2127 2.21 5 O 2202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 616": "NH1" <-> "NH2" Residue "A ARG 702": "NH1" <-> "NH2" Residue "A PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1274": "NH1" <-> "NH2" Residue "A PHE 1338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B GLU 333": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12244 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9318 Classifications: {'peptide': 1175} Link IDs: {'PTRANS': 66, 'TRANS': 1108} Chain breaks: 12 Chain: "B" Number of atoms: 2926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2926 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 15, 'TRANS': 347} Time building chain proxies: 6.61, per 1000 atoms: 0.54 Number of scatterers: 12244 At special positions: 0 Unit cell: (88.81, 135.89, 102.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 2202 8.00 N 2127 7.00 C 7841 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.90 Conformation dependent library (CDL) restraints added in 2.3 seconds 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2880 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 36 sheets defined 5.8% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 487 through 491 removed outlier: 3.616A pdb=" N GLN A 491 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 1153 through 1156 Processing helix chain 'A' and resid 1352 through 1369 removed outlier: 3.777A pdb=" N ARG A1358 " --> pdb=" O LYS A1354 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A1359 " --> pdb=" O THR A1355 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1376 removed outlier: 3.552A pdb=" N LEU A1376 " --> pdb=" O HIS A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1382 Processing helix chain 'A' and resid 1403 through 1407 Processing helix chain 'A' and resid 1414 through 1423 removed outlier: 3.897A pdb=" N LEU A1418 " --> pdb=" O GLU A1414 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1440 removed outlier: 4.010A pdb=" N ILE A1429 " --> pdb=" O THR A1425 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A1435 " --> pdb=" O ASP A1431 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR A1436 " --> pdb=" O ASP A1432 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A1440 " --> pdb=" O THR A1436 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 71 removed outlier: 4.033A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1349 through 1350 Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 9 removed outlier: 6.209A pdb=" N ILE A1345 " --> pdb=" O ALA A 8 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 14 through 20 removed outlier: 4.077A pdb=" N GLN A 37 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ARG A 42 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU A 68 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN A 44 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU A 66 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 80 through 82 removed outlier: 3.759A pdb=" N LYS A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU A 103 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU A 120 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 105 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 140 through 143 Processing sheet with id=AA6, first strand: chain 'A' and resid 205 through 208 removed outlier: 3.855A pdb=" N ASP A 205 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 265 through 270 removed outlier: 4.296A pdb=" N GLN A 267 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER A 285 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N GLY A 297 " --> pdb=" O ARG A 313 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 326 through 330 removed outlier: 4.122A pdb=" N LYS A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR A 348 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N PHE A 360 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE A 350 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 326 through 330 removed outlier: 4.122A pdb=" N LYS A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE A 344 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 375 through 377 removed outlier: 3.555A pdb=" N LEU A 392 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 478 through 481 Processing sheet with id=AB3, first strand: chain 'A' and resid 522 through 526 removed outlier: 5.282A pdb=" N VAL A 523 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A1000 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 525 " --> pdb=" O ILE A 998 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR A 989 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER A 974 " --> pdb=" O PHE A 990 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 532 through 539 removed outlier: 3.914A pdb=" N ASP A 534 " --> pdb=" O SER A 578 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 608 through 612 removed outlier: 3.682A pdb=" N PHE A 608 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 646 through 650 removed outlier: 3.616A pdb=" N GLN A 648 " --> pdb=" O MET A 659 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 670 through 671 Processing sheet with id=AB8, first strand: chain 'A' and resid 695 through 702 removed outlier: 7.020A pdb=" N VAL A 788 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU A 698 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 786 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU A 700 " --> pdb=" O TRP A 784 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TRP A 784 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET A 794 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU A 807 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 796 " --> pdb=" O VAL A 805 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 846 through 854 removed outlier: 6.502A pdb=" N HIS A 866 " --> pdb=" O LYS A 847 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL A 849 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 864 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU A 851 " --> pdb=" O TYR A 862 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR A 862 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ALA A 853 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG A 860 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 865 " --> pdb=" O LEU A 872 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU A 872 " --> pdb=" O VAL A 865 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 877 through 878 Processing sheet with id=AC2, first strand: chain 'A' and resid 931 through 937 removed outlier: 5.469A pdb=" N TYR A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1022 through 1028 removed outlier: 3.669A pdb=" N TYR A1024 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A1033 " --> pdb=" O HIS A1028 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1041 through 1043 Processing sheet with id=AC5, first strand: chain 'A' and resid 1046 through 1050 Processing sheet with id=AC6, first strand: chain 'A' and resid 1098 through 1106 removed outlier: 6.733A pdb=" N GLY A1124 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N MET A1103 " --> pdb=" O ALA A1122 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ALA A1122 " --> pdb=" O MET A1103 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N THR A1105 " --> pdb=" O TYR A1120 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N TYR A1120 " --> pdb=" O THR A1105 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY A1137 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU A1167 " --> pdb=" O GLY A1137 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE A1139 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU A1165 " --> pdb=" O ILE A1139 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A1141 " --> pdb=" O LEU A1163 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1176 through 1178 removed outlier: 6.956A pdb=" N LEU A1192 " --> pdb=" O MET A1203 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A1203 " --> pdb=" O LEU A1192 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1212 through 1217 removed outlier: 3.662A pdb=" N GLN A1214 " --> pdb=" O ALA A1225 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1233 through 1237 removed outlier: 7.228A pdb=" N LEU A1233 " --> pdb=" O VAL A1246 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR A1242 " --> pdb=" O GLN A1237 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1257 through 1258 removed outlier: 3.700A pdb=" N SER A1257 " --> pdb=" O SER A1272 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1257 through 1258 removed outlier: 3.700A pdb=" N SER A1257 " --> pdb=" O SER A1272 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU A1278 " --> pdb=" O ASP A1301 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP A1301 " --> pdb=" O LEU A1278 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A1280 " --> pdb=" O ARG A1299 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 109 through 113 removed outlier: 6.655A pdb=" N PHE B 401 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS B 400 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE B 389 " --> pdb=" O TRP B 383 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TRP B 383 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS B 391 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU B 381 " --> pdb=" O CYS B 391 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY B 393 " --> pdb=" O TRP B 379 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 122 through 127 removed outlier: 3.573A pdb=" N VAL B 124 " --> pdb=" O GLY B 137 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 167 through 169 removed outlier: 6.999A pdb=" N VAL B 185 " --> pdb=" O MET B 197 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N MET B 197 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR B 187 " --> pdb=" O VAL B 195 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 205 through 210 removed outlier: 7.064A pdb=" N CYS B 220 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA B 208 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA B 218 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE B 210 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS B 216 " --> pdb=" O PHE B 210 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 226 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 238 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP B 230 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLU B 236 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 250 through 252 removed outlier: 3.510A pdb=" N ALA B 282 " --> pdb=" O PHE B 272 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 291 through 296 Processing sheet with id=AD9, first strand: chain 'B' and resid 338 through 339 removed outlier: 3.849A pdb=" N GLY B 368 " --> pdb=" O PHE B 358 " (cutoff:3.500A) 325 hydrogen bonds defined for protein. 834 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.43 Time building geometry restraints manager: 5.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3837 1.33 - 1.45: 1951 1.45 - 1.57: 6636 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 12544 Sorted by residual: bond pdb=" CA ASN B 101 " pdb=" C ASN B 101 " ideal model delta sigma weight residual 1.532 1.507 0.025 6.50e-03 2.37e+04 1.48e+01 bond pdb=" CA VAL B 106 " pdb=" C VAL B 106 " ideal model delta sigma weight residual 1.524 1.498 0.026 8.60e-03 1.35e+04 9.36e+00 bond pdb=" CA PRO B 95 " pdb=" C PRO B 95 " ideal model delta sigma weight residual 1.521 1.554 -0.033 1.25e-02 6.40e+03 7.13e+00 bond pdb=" CA ASN A 202 " pdb=" C ASN A 202 " ideal model delta sigma weight residual 1.522 1.491 0.030 1.20e-02 6.94e+03 6.38e+00 bond pdb=" C ASN B 101 " pdb=" O ASN B 101 " ideal model delta sigma weight residual 1.233 1.222 0.011 4.80e-03 4.34e+04 5.43e+00 ... (remaining 12539 not shown) Histogram of bond angle deviations from ideal: 97.81 - 105.06: 302 105.06 - 112.31: 6318 112.31 - 119.56: 4055 119.56 - 126.81: 6135 126.81 - 134.06: 212 Bond angle restraints: 17022 Sorted by residual: angle pdb=" C ASN B 101 " pdb=" N PRO B 102 " pdb=" CA PRO B 102 " ideal model delta sigma weight residual 119.56 130.38 -10.82 1.02e+00 9.61e-01 1.13e+02 angle pdb=" C VAL B 106 " pdb=" CA VAL B 106 " pdb=" CB VAL B 106 " ideal model delta sigma weight residual 113.22 102.63 10.59 1.12e+00 7.97e-01 8.94e+01 angle pdb=" C ASP A 653 " pdb=" N PRO A 654 " pdb=" CA PRO A 654 " ideal model delta sigma weight residual 119.84 130.10 -10.26 1.25e+00 6.40e-01 6.74e+01 angle pdb=" N LEU A 624 " pdb=" CA LEU A 624 " pdb=" C LEU A 624 " ideal model delta sigma weight residual 111.36 119.87 -8.51 1.09e+00 8.42e-01 6.09e+01 angle pdb=" N ALA A 232 " pdb=" CA ALA A 232 " pdb=" C ALA A 232 " ideal model delta sigma weight residual 114.62 106.38 8.24 1.14e+00 7.69e-01 5.23e+01 ... (remaining 17017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.37: 6929 14.37 - 28.73: 408 28.73 - 43.10: 93 43.10 - 57.46: 27 57.46 - 71.83: 8 Dihedral angle restraints: 7465 sinusoidal: 3009 harmonic: 4456 Sorted by residual: dihedral pdb=" C HIS A1385 " pdb=" N HIS A1385 " pdb=" CA HIS A1385 " pdb=" CB HIS A1385 " ideal model delta harmonic sigma weight residual -122.60 -137.45 14.85 0 2.50e+00 1.60e-01 3.53e+01 dihedral pdb=" CA SER A1272 " pdb=" C SER A1272 " pdb=" N ASP A1273 " pdb=" CA ASP A1273 " ideal model delta harmonic sigma weight residual 180.00 -150.36 -29.64 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" N HIS A1385 " pdb=" C HIS A1385 " pdb=" CA HIS A1385 " pdb=" CB HIS A1385 " ideal model delta harmonic sigma weight residual 122.80 137.52 -14.72 0 2.50e+00 1.60e-01 3.47e+01 ... (remaining 7462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 1826 0.136 - 0.272: 67 0.272 - 0.407: 4 0.407 - 0.543: 3 0.543 - 0.679: 1 Chirality restraints: 1901 Sorted by residual: chirality pdb=" CA HIS A1385 " pdb=" N HIS A1385 " pdb=" C HIS A1385 " pdb=" CB HIS A1385 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" CA ASP A 333 " pdb=" N ASP A 333 " pdb=" C ASP A 333 " pdb=" CB ASP A 333 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.54 2.00e-01 2.50e+01 7.16e+00 chirality pdb=" CA ASN A1220 " pdb=" N ASN A1220 " pdb=" C ASN A1220 " pdb=" CB ASN A1220 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 1898 not shown) Planarity restraints: 2169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 653 " 0.064 5.00e-02 4.00e+02 9.50e-02 1.44e+01 pdb=" N PRO A 654 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO A 654 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 654 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A1382 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C ARG A1382 " 0.056 2.00e-02 2.50e+03 pdb=" O ARG A1382 " -0.021 2.00e-02 2.50e+03 pdb=" N MET A1383 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1312 " -0.032 2.00e-02 2.50e+03 1.90e-02 9.06e+00 pdb=" CG TRP A1312 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP A1312 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A1312 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A1312 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1312 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A1312 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1312 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1312 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A1312 " -0.007 2.00e-02 2.50e+03 ... (remaining 2166 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 105 2.56 - 3.15: 8948 3.15 - 3.73: 17870 3.73 - 4.32: 26018 4.32 - 4.90: 44191 Nonbonded interactions: 97132 Sorted by model distance: nonbonded pdb=" OD1 ASP B 396 " pdb=" N HIS B 397 " model vdw 1.978 2.520 nonbonded pdb=" N GLU B 333 " pdb=" OE1 GLU B 333 " model vdw 2.077 2.520 nonbonded pdb=" O MET B 103 " pdb=" O ASN B 104 " model vdw 2.115 3.040 nonbonded pdb=" O PHE A 811 " pdb=" O PRO A 812 " model vdw 2.166 3.040 nonbonded pdb=" O SER A 302 " pdb=" OG SER A 302 " model vdw 2.174 2.440 ... (remaining 97127 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 0.010 Extract box with map and model: 2.290 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 40.430 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 : 0.007 0.069 12544 Z= 0.447 Angle : 1.092 12.329 17022 Z= 0.643 Chirality : 0.067 0.679 1901 Planarity : 0.008 0.095 2169 Dihedral : 10.665 71.831 4585 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.93 % Allowed : 8.94 % Favored : 90.13 % Rotamer: Outliers : 2.83 % Allowed : 2.68 % Favored : 94.49 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % 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: -3.90 (0.18), residues: 1510 helix: -4.68 (0.16), residues: 89 sheet: -1.98 (0.19), residues: 589 loop : -2.85 (0.18), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP A1312 HIS 0.013 0.002 HIS B 171 PHE 0.032 0.004 PHE A 72 TYR 0.029 0.003 TYR A 2 ARG 0.010 0.001 ARG A 932 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 438 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 TYR cc_start: 0.8463 (p90) cc_final: 0.8002 (p90) REVERT: A 202 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7368 (m-40) REVERT: A 523 VAL cc_start: 0.8636 (t) cc_final: 0.7099 (t) REVERT: A 996 LEU cc_start: 0.8234 (tp) cc_final: 0.7931 (tt) REVERT: A 1183 VAL cc_start: 0.8936 (t) cc_final: 0.8706 (t) REVERT: A 1220 ASN cc_start: 0.7113 (OUTLIER) cc_final: 0.6459 (t0) REVERT: A 1259 ASP cc_start: 0.7142 (t0) cc_final: 0.6695 (t0) REVERT: A 1277 ASN cc_start: 0.8202 (m-40) cc_final: 0.7996 (m-40) REVERT: A 1386 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7431 (p) REVERT: B 353 ASP cc_start: 0.6342 (p0) cc_final: 0.5771 (p0) REVERT: B 403 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8384 (t) outliers start: 38 outliers final: 7 residues processed: 467 average time/residue: 0.3117 time to fit residues: 201.2993 Evaluate side-chains 242 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 231 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 227 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 1220 ASN Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1385 HIS Chi-restraints excluded: chain A residue 1386 VAL Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 403 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 0.0270 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 225 GLN ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 GLN A 634 GLN A 648 GLN A 866 HIS A 879 HIS ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1442 HIS B 69 ASN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 116 ASN ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN B 325 GLN ** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 12544 Z= 0.229 Angle : 0.746 11.578 17022 Z= 0.379 Chirality : 0.048 0.264 1901 Planarity : 0.006 0.103 2169 Dihedral : 6.991 58.454 1685 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.23 % Favored : 93.31 % Rotamer: Outliers : 3.65 % Allowed : 13.63 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.10 (0.19), residues: 1510 helix: -2.96 (0.40), residues: 84 sheet: -1.36 (0.20), residues: 597 loop : -2.55 (0.18), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1337 HIS 0.013 0.001 HIS B 397 PHE 0.021 0.002 PHE B 217 TYR 0.028 0.002 TYR A 19 ARG 0.006 0.001 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 264 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 TYR cc_start: 0.8388 (p90) cc_final: 0.8167 (p90) REVERT: A 480 VAL cc_start: 0.9292 (t) cc_final: 0.9084 (m) REVERT: A 498 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8306 (pp) REVERT: A 707 MET cc_start: 0.8154 (ptp) cc_final: 0.7947 (ptp) REVERT: A 996 LEU cc_start: 0.8563 (tp) cc_final: 0.8260 (tt) REVERT: A 1209 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7415 (mt0) REVERT: A 1220 ASN cc_start: 0.7403 (OUTLIER) cc_final: 0.6798 (t0) REVERT: B 192 MET cc_start: 0.6956 (mmt) cc_final: 0.6613 (mmp) REVERT: B 210 PHE cc_start: 0.7174 (OUTLIER) cc_final: 0.6943 (p90) REVERT: B 320 LEU cc_start: 0.6165 (mt) cc_final: 0.5944 (mt) REVERT: B 353 ASP cc_start: 0.5984 (p0) cc_final: 0.5362 (p0) outliers start: 49 outliers final: 30 residues processed: 300 average time/residue: 0.2196 time to fit residues: 98.6069 Evaluate side-chains 231 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 197 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 227 TRP Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 1029 VAL Chi-restraints excluded: chain A residue 1093 GLU Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain A residue 1220 ASN Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1351 MET Chi-restraints excluded: chain A residue 1385 HIS Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 346 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 115 optimal weight: 0.3980 chunk 94 optimal weight: 0.5980 chunk 38 optimal weight: 0.0870 chunk 139 optimal weight: 0.9990 chunk 150 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN B 325 GLN ** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 12544 Z= 0.187 Angle : 0.660 10.295 17022 Z= 0.335 Chirality : 0.046 0.207 1901 Planarity : 0.005 0.104 2169 Dihedral : 6.491 56.236 1683 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.29 % Favored : 93.38 % Rotamer: Outliers : 3.20 % Allowed : 15.86 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.57 (0.20), residues: 1510 helix: -1.94 (0.50), residues: 82 sheet: -0.92 (0.20), residues: 582 loop : -2.32 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A1097 HIS 0.008 0.001 HIS B 397 PHE 0.024 0.002 PHE A 221 TYR 0.020 0.002 TYR A 213 ARG 0.014 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 219 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 TYR cc_start: 0.8378 (p90) cc_final: 0.8142 (p90) REVERT: A 498 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8371 (pp) REVERT: A 996 LEU cc_start: 0.8587 (tp) cc_final: 0.8250 (tt) REVERT: B 192 MET cc_start: 0.7000 (mmt) cc_final: 0.6639 (mmp) REVERT: B 320 LEU cc_start: 0.6387 (mt) cc_final: 0.5984 (mp) REVERT: B 353 ASP cc_start: 0.6158 (p0) cc_final: 0.5622 (p0) outliers start: 43 outliers final: 29 residues processed: 243 average time/residue: 0.2094 time to fit residues: 77.4641 Evaluate side-chains 212 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 182 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 227 TRP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1093 GLU Chi-restraints excluded: chain A residue 1221 PHE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1297 LEU Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1351 MET Chi-restraints excluded: chain A residue 1385 HIS Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 346 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 15 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 HIS ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 GLN A1332 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.139 12544 Z= 0.543 Angle : 0.804 9.282 17022 Z= 0.411 Chirality : 0.050 0.191 1901 Planarity : 0.006 0.113 2169 Dihedral : 6.569 56.098 1680 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.68 % Favored : 91.92 % Rotamer: Outliers : 5.36 % Allowed : 14.82 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.42 (0.20), residues: 1510 helix: -1.47 (0.53), residues: 82 sheet: -1.06 (0.20), residues: 603 loop : -2.07 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP A1097 HIS 0.014 0.002 HIS A 9 PHE 0.030 0.003 PHE A 221 TYR 0.019 0.002 TYR B 187 ARG 0.010 0.001 ARG A 627 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 193 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8478 (pp) REVERT: A 1208 THR cc_start: 0.8632 (t) cc_final: 0.8225 (t) outliers start: 72 outliers final: 48 residues processed: 245 average time/residue: 0.2024 time to fit residues: 77.9359 Evaluate side-chains 211 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 162 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 227 TRP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 897 HIS Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 946 CYS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1093 GLU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1220 ASN Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1297 LEU Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 346 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 HIS ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN B 397 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 12544 Z= 0.227 Angle : 0.662 9.181 17022 Z= 0.336 Chirality : 0.046 0.199 1901 Planarity : 0.005 0.111 2169 Dihedral : 6.098 56.033 1676 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.95 % Favored : 92.78 % Rotamer: Outliers : 3.65 % Allowed : 17.42 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.16 (0.20), residues: 1510 helix: -1.15 (0.54), residues: 82 sheet: -0.70 (0.21), residues: 572 loop : -2.04 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A1097 HIS 0.007 0.001 HIS A 685 PHE 0.023 0.002 PHE B 217 TYR 0.031 0.002 TYR A 19 ARG 0.011 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 179 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ILE cc_start: 0.8548 (mm) cc_final: 0.8248 (mm) REVERT: A 256 TRP cc_start: 0.8371 (t60) cc_final: 0.8121 (t60) REVERT: A 1208 THR cc_start: 0.8456 (t) cc_final: 0.8190 (t) REVERT: B 192 MET cc_start: 0.7094 (mmt) cc_final: 0.6809 (mmp) outliers start: 49 outliers final: 35 residues processed: 211 average time/residue: 0.1846 time to fit residues: 62.3951 Evaluate side-chains 198 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 227 TRP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 633 ASN Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 897 HIS Chi-restraints excluded: chain A residue 946 CYS Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 346 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 86 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 12544 Z= 0.326 Angle : 0.691 10.442 17022 Z= 0.348 Chirality : 0.047 0.204 1901 Planarity : 0.005 0.112 2169 Dihedral : 6.041 58.066 1676 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.01 % Favored : 91.72 % Rotamer: Outliers : 4.47 % Allowed : 17.42 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.04 (0.21), residues: 1510 helix: -0.88 (0.54), residues: 82 sheet: -0.64 (0.21), residues: 585 loop : -1.97 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A1097 HIS 0.029 0.001 HIS B 181 PHE 0.023 0.002 PHE A 221 TYR 0.030 0.002 TYR A 19 ARG 0.007 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 174 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 TRP cc_start: 0.8345 (t60) cc_final: 0.8089 (t60) outliers start: 60 outliers final: 49 residues processed: 211 average time/residue: 0.1966 time to fit residues: 65.4885 Evaluate side-chains 212 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 163 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 227 TRP Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 633 ASN Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 897 HIS Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 946 CYS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 346 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 147 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 12544 Z= 0.255 Angle : 0.660 9.769 17022 Z= 0.332 Chirality : 0.047 0.282 1901 Planarity : 0.005 0.112 2169 Dihedral : 5.783 54.844 1676 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.15 % Favored : 92.58 % Rotamer: Outliers : 4.10 % Allowed : 18.17 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.93 (0.21), residues: 1510 helix: -0.48 (0.57), residues: 81 sheet: -0.58 (0.21), residues: 583 loop : -1.92 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A1097 HIS 0.006 0.001 HIS A 685 PHE 0.022 0.002 PHE B 217 TYR 0.028 0.001 TYR A 19 ARG 0.014 0.001 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 179 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.7396 (t0) REVERT: A 203 ILE cc_start: 0.8563 (mm) cc_final: 0.8292 (mm) REVERT: A 256 TRP cc_start: 0.8260 (t60) cc_final: 0.7898 (t60) REVERT: A 1105 THR cc_start: 0.9017 (m) cc_final: 0.8429 (t) REVERT: B 210 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6083 (p90) outliers start: 55 outliers final: 42 residues processed: 214 average time/residue: 0.1932 time to fit residues: 65.5908 Evaluate side-chains 211 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 167 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 897 HIS Chi-restraints excluded: chain A residue 946 CYS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1297 LEU Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 346 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 12544 Z= 0.422 Angle : 0.731 11.369 17022 Z= 0.367 Chirality : 0.049 0.414 1901 Planarity : 0.005 0.114 2169 Dihedral : 5.729 54.207 1670 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.87 % Favored : 90.86 % Rotamer: Outliers : 4.32 % Allowed : 18.24 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.95 (0.21), residues: 1510 helix: -0.43 (0.58), residues: 81 sheet: -0.62 (0.21), residues: 577 loop : -1.92 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A1097 HIS 0.022 0.002 HIS A 252 PHE 0.023 0.002 PHE A 221 TYR 0.035 0.002 TYR A 19 ARG 0.009 0.001 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 165 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 THR cc_start: 0.8401 (m) cc_final: 0.8135 (t) REVERT: A 256 TRP cc_start: 0.8317 (t60) cc_final: 0.8002 (t60) REVERT: A 1105 THR cc_start: 0.9088 (m) cc_final: 0.8519 (t) REVERT: B 210 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6275 (p90) outliers start: 58 outliers final: 50 residues processed: 205 average time/residue: 0.1960 time to fit residues: 63.2625 Evaluate side-chains 209 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 158 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 897 HIS Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 946 CYS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1125 THR Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1231 ILE Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1297 LEU Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 346 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 82 optimal weight: 0.0670 chunk 59 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1214 GLN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN B 405 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 12544 Z= 0.197 Angle : 0.646 10.047 17022 Z= 0.323 Chirality : 0.047 0.274 1901 Planarity : 0.005 0.111 2169 Dihedral : 5.338 38.754 1668 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.89 % Favored : 92.85 % Rotamer: Outliers : 3.05 % Allowed : 19.96 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.21), residues: 1510 helix: -0.14 (0.59), residues: 81 sheet: -0.45 (0.22), residues: 573 loop : -1.84 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A1097 HIS 0.004 0.001 HIS B 201 PHE 0.022 0.002 PHE A 221 TYR 0.037 0.002 TYR A 19 ARG 0.009 0.001 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 186 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 TYR cc_start: 0.8146 (p90) cc_final: 0.7930 (p90) REVERT: A 256 TRP cc_start: 0.8179 (t60) cc_final: 0.7782 (t60) REVERT: A 1105 THR cc_start: 0.8987 (m) cc_final: 0.8428 (t) REVERT: B 210 PHE cc_start: 0.6761 (OUTLIER) cc_final: 0.5885 (p90) outliers start: 41 outliers final: 35 residues processed: 212 average time/residue: 0.2164 time to fit residues: 70.3705 Evaluate side-chains 202 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 166 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 897 HIS Chi-restraints excluded: chain A residue 946 CYS Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1214 GLN Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 378 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 121 optimal weight: 0.0060 chunk 12 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 HIS ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 12544 Z= 0.205 Angle : 0.669 11.892 17022 Z= 0.332 Chirality : 0.047 0.271 1901 Planarity : 0.005 0.109 2169 Dihedral : 5.258 35.905 1668 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.48 % Favored : 92.25 % Rotamer: Outliers : 2.90 % Allowed : 20.77 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.70 (0.21), residues: 1510 helix: 0.02 (0.61), residues: 81 sheet: -0.36 (0.22), residues: 565 loop : -1.83 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A1097 HIS 0.012 0.001 HIS A1213 PHE 0.033 0.002 PHE A 221 TYR 0.035 0.001 TYR A 19 ARG 0.010 0.000 ARG A 358 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 185 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 TYR cc_start: 0.8159 (p90) cc_final: 0.7940 (p90) REVERT: A 203 ILE cc_start: 0.8627 (mm) cc_final: 0.8390 (mm) REVERT: A 252 HIS cc_start: 0.8660 (OUTLIER) cc_final: 0.8126 (m170) REVERT: A 256 TRP cc_start: 0.8131 (t60) cc_final: 0.7711 (t60) REVERT: A 685 HIS cc_start: 0.6401 (OUTLIER) cc_final: 0.6188 (m170) REVERT: A 1105 THR cc_start: 0.8977 (m) cc_final: 0.8415 (t) REVERT: B 210 PHE cc_start: 0.6692 (OUTLIER) cc_final: 0.5951 (p90) outliers start: 39 outliers final: 33 residues processed: 209 average time/residue: 0.2054 time to fit residues: 66.0333 Evaluate side-chains 211 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 175 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 685 HIS Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 897 HIS Chi-restraints excluded: chain A residue 946 CYS Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1261 MET Chi-restraints excluded: chain A residue 1297 LEU Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 378 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 6.9990 chunk 37 optimal weight: 0.1980 chunk 111 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 121 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 chunk 106 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 HIS ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.099911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.081154 restraints weight = 22296.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.083840 restraints weight = 12634.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.085722 restraints weight = 8625.603| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.6012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 12544 Z= 0.196 Angle : 0.649 10.307 17022 Z= 0.324 Chirality : 0.046 0.265 1901 Planarity : 0.005 0.113 2169 Dihedral : 5.185 34.271 1668 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.22 % Favored : 92.52 % Rotamer: Outliers : 2.76 % Allowed : 21.00 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.68 (0.21), residues: 1510 helix: 0.06 (0.60), residues: 81 sheet: -0.38 (0.22), residues: 569 loop : -1.81 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A1097 HIS 0.013 0.001 HIS A 252 PHE 0.041 0.002 PHE A 221 TYR 0.033 0.001 TYR A 19 ARG 0.010 0.000 ARG A 358 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2602.78 seconds wall clock time: 48 minutes 24.35 seconds (2904.35 seconds total)