Starting phenix.real_space_refine (version: dev) on Mon Dec 12 21:24:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bm0_7114/12_2022/6bm0_7114.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bm0_7114/12_2022/6bm0_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_7114/12_2022/6bm0_7114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bm0_7114/12_2022/6bm0_7114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bm0_7114/12_2022/6bm0_7114.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bm0_7114/12_2022/6bm0_7114.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 7.27, per 1000 atoms: 0.59 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: 4.74 Conformation dependent library (CDL) restraints added in 1.9 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: 1.09 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: 5.49 Time building geometry restraints manager: 5.18 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 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. 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: 0.220 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: 2.710 Check model and map are aligned: 0.190 Convert atoms to be neutral: 0.100 Process input model: 35.890 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 : 19.31 Ramachandran Plot: Outliers : 0.93 % Allowed : 8.94 % Favored : 90.13 % Rotamer Outliers : 2.83 % 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 *********************** 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 : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 7 residues processed: 467 average time/residue: 0.2681 time to fit residues: 172.9742 Evaluate side-chains 235 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 228 time to evaluate : 1.547 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.1206 time to fit residues: 3.5684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 0.0270 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 284 ASN A 620 GLN A 634 GLN A 648 GLN A 866 HIS A 879 HIS ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1220 ASN A1442 HIS B 69 ASN B 83 GLN 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 12544 Z= 0.224 Angle : 0.754 10.819 17022 Z= 0.384 Chirality : 0.049 0.269 1901 Planarity : 0.006 0.103 2169 Dihedral : 6.153 25.019 1666 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.42 % Favored : 93.11 % Rotamer Outliers : 2.90 % 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: -3.13 (0.19), residues: 1510 helix: -2.96 (0.40), residues: 84 sheet: -1.38 (0.20), residues: 597 loop : -2.56 (0.18), residues: 829 *********************** 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 304 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 265 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 24 residues processed: 294 average time/residue: 0.2182 time to fit residues: 95.7645 Evaluate side-chains 222 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 198 time to evaluate : 1.421 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1158 time to fit residues: 7.0947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 115 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 chunk 139 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 47 optimal weight: 0.4980 chunk 111 optimal weight: 4.9990 overall best weight: 1.9144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN ** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 12544 Z= 0.280 Angle : 0.698 9.450 17022 Z= 0.355 Chirality : 0.047 0.224 1901 Planarity : 0.005 0.107 2169 Dihedral : 5.714 25.362 1666 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.82 % Favored : 92.85 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.60 (0.20), residues: 1510 helix: -1.90 (0.51), residues: 82 sheet: -1.07 (0.20), residues: 603 loop : -2.25 (0.19), residues: 825 *********************** 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 242 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 212 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 228 average time/residue: 0.2085 time to fit residues: 72.7245 Evaluate side-chains 198 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 180 time to evaluate : 1.490 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1163 time to fit residues: 5.9368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 0.0770 chunk 66 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 202 ASN ** A 284 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** A 783 HIS ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1442 HIS B 69 ASN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN ** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.073 12544 Z= 0.365 Angle : 0.722 9.484 17022 Z= 0.366 Chirality : 0.048 0.218 1901 Planarity : 0.006 0.112 2169 Dihedral : 5.593 23.059 1666 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.35 % Favored : 92.32 % Rotamer Outliers : 3.43 % 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: -2.39 (0.20), residues: 1510 helix: -1.33 (0.54), residues: 82 sheet: -1.00 (0.20), residues: 602 loop : -2.09 (0.20), residues: 826 *********************** 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 235 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 189 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 23 residues processed: 217 average time/residue: 0.1979 time to fit residues: 67.0933 Evaluate side-chains 185 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 162 time to evaluate : 1.372 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1111 time to fit residues: 6.6916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 75 optimal weight: 0.0570 chunk 132 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 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 405 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.5036 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= 0.240 Angle : 0.668 9.466 17022 Z= 0.336 Chirality : 0.046 0.210 1901 Planarity : 0.005 0.111 2169 Dihedral : 5.356 21.868 1666 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.09 % Favored : 92.65 % Rotamer Outliers : 1.71 % 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: -2.18 (0.21), residues: 1510 helix: -1.04 (0.55), residues: 82 sheet: -0.77 (0.21), residues: 597 loop : -2.05 (0.20), residues: 831 *********************** 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 210 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 187 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 201 average time/residue: 0.1946 time to fit residues: 62.4760 Evaluate side-chains 176 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 1.467 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1120 time to fit residues: 4.4300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 86 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 0.2980 chunk 142 optimal weight: 9.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN ** A 509 ASN ** 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 B 397 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5206 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= 0.185 Angle : 0.643 11.761 17022 Z= 0.318 Chirality : 0.046 0.207 1901 Planarity : 0.005 0.109 2169 Dihedral : 5.155 21.071 1666 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.49 % Favored : 93.25 % Rotamer Outliers : 1.56 % 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: -1.97 (0.21), residues: 1510 helix: -0.71 (0.57), residues: 82 sheet: -0.58 (0.21), residues: 605 loop : -1.98 (0.21), residues: 823 *********************** 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 214 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 193 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 7 residues processed: 205 average time/residue: 0.2090 time to fit residues: 66.8309 Evaluate side-chains 179 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 172 time to evaluate : 1.487 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1300 time to fit residues: 3.6561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 ** 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: 0.8199 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 12544 Z= 0.357 Angle : 0.691 10.623 17022 Z= 0.348 Chirality : 0.047 0.220 1901 Planarity : 0.005 0.112 2169 Dihedral : 5.343 22.324 1666 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.95 % Favored : 91.79 % Rotamer Outliers : 2.31 % 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: -0.60 (0.56), residues: 81 sheet: -0.56 (0.21), residues: 587 loop : -1.93 (0.21), residues: 842 *********************** 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 206 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 175 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 21 residues processed: 192 average time/residue: 0.2172 time to fit residues: 63.8502 Evaluate side-chains 178 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 157 time to evaluate : 1.462 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1349 time to fit residues: 6.9444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1209 GLN ** 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: 0.8253 moved from start: 0.5966 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= 0.423 Angle : 0.748 11.704 17022 Z= 0.375 Chirality : 0.049 0.273 1901 Planarity : 0.006 0.116 2169 Dihedral : 5.625 24.884 1666 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.74 % Favored : 90.99 % Rotamer Outliers : 1.27 % 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: -2.01 (0.21), residues: 1510 helix: -0.42 (0.59), residues: 81 sheet: -0.75 (0.21), residues: 598 loop : -1.90 (0.21), residues: 831 *********************** 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 185 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 176 average time/residue: 0.2146 time to fit residues: 59.1893 Evaluate side-chains 166 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 154 time to evaluate : 1.501 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1271 time to fit residues: 4.8213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 GLN A 685 HIS ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1209 GLN ** 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: 0.8210 moved from start: 0.6090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 12544 Z= 0.270 Angle : 0.691 10.049 17022 Z= 0.344 Chirality : 0.047 0.282 1901 Planarity : 0.005 0.114 2169 Dihedral : 5.410 22.363 1666 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.88 % Favored : 91.92 % Rotamer Outliers : 1.04 % 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: -0.13 (0.60), residues: 81 sheet: -0.66 (0.22), residues: 587 loop : -1.89 (0.21), residues: 842 *********************** 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 185 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 178 average time/residue: 0.2382 time to fit residues: 64.3985 Evaluate side-chains 173 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 1.457 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1361 time to fit residues: 4.3717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 0.0000 chunk 101 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 509 ASN A 685 HIS ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1214 GLN B 116 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.6137 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= 0.205 Angle : 0.679 10.569 17022 Z= 0.336 Chirality : 0.046 0.287 1901 Planarity : 0.005 0.112 2169 Dihedral : 5.193 22.093 1666 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.28 % Favored : 92.52 % Rotamer Outliers : 0.45 % 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: -1.79 (0.21), residues: 1510 helix: 0.09 (0.61), residues: 81 sheet: -0.51 (0.22), residues: 568 loop : -1.85 (0.21), residues: 861 ********************** 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 187 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 181 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 183 average time/residue: 0.2230 time to fit residues: 62.5735 Evaluate side-chains 170 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 1.403 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1581 time to fit residues: 2.6287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 5.9990 chunk 37 optimal weight: 0.0470 chunk 111 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 121 optimal weight: 0.0870 chunk 50 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.9858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 685 HIS ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3120 r_free = 0.3120 target = 0.097707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.079347 restraints weight = 22605.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.081999 restraints weight = 12755.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.083810 restraints weight = 8677.768| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.6226 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= 0.214 Angle : 0.674 10.438 17022 Z= 0.332 Chirality : 0.047 0.288 1901 Planarity : 0.005 0.110 2169 Dihedral : 5.136 21.947 1666 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.02 % Favored : 92.78 % Rotamer Outliers : 0.45 % 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: -1.73 (0.22), residues: 1510 helix: 0.17 (0.62), residues: 81 sheet: -0.46 (0.22), residues: 570 loop : -1.82 (0.21), residues: 859 =============================================================================== Job complete usr+sys time: 2397.75 seconds wall clock time: 44 minutes 38.18 seconds (2678.18 seconds total)