Starting phenix.real_space_refine on Fri Sep 11 23:00:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yi2_33849/09_2026/7yi2_33849.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yi2_33849/09_2026/7yi2_33849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yi2_33849/09_2026/7yi2_33849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yi2_33849/09_2026/7yi2_33849.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yi2_33849/09_2026/7yi2_33849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yi2_33849/09_2026/7yi2_33849.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yi2_33849/09_2026/7yi2_33849.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yi2_33849/09_2026/7yi2_33849.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 P 33 5.49 5 S 66 5.16 5 C 7644 2.51 5 N 2051 2.21 5 O 2341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12140 Number of models: 1 Model: "" Number of chains: 9 Chain: "G" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "H" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 347 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 4258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4258 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 7, 'TRANS': 498} Chain breaks: 5 Chain: "B" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2923 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "C" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1473 Classifications: {'peptide': 182} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 174} Chain: "D" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2626 Classifications: {'peptide': 321} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 302} Chain breaks: 5 Chain: "E" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 178 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9823 SG CYS D 263 45.192 98.283 35.197 1.00 82.35 S ATOM 9840 SG CYS D 266 47.386 95.169 34.847 1.00 75.72 S ATOM 9993 SG CYS D 286 48.607 98.051 37.042 1.00 87.95 S ATOM 9925 SG CYS D 278 37.477 107.248 31.247 1.00102.60 S ATOM 10151 SG CYS D 306 37.138 109.944 30.588 1.00 95.03 S ATOM 11072 SG CYS D 440 68.674 66.827 27.274 1.00 44.61 S ATOM 11098 SG CYS D 443 71.466 66.135 24.692 1.00 57.38 S ATOM 11287 SG CYS D 466 72.291 66.083 28.297 1.00 69.65 S ATOM 10884 SG CYS D 417 71.804 56.226 31.155 1.00 48.05 S ATOM 10911 SG CYS D 420 72.125 52.570 32.298 1.00 70.53 S ATOM 11167 SG CYS D 451 72.311 55.368 34.881 1.00 47.98 S Time building chain proxies: 2.83, per 1000 atoms: 0.23 Number of scatterers: 12140 At special positions: 0 Unit cell: (125.57, 139.643, 101.755, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 S 66 16.00 P 33 15.00 O 2341 8.00 N 2051 7.00 C 7644 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 612.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 188 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" ND1 HIS D 283 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 266 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 263 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 286 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 278 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 306 " pdb=" ZN D 703 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 469 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 466 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 443 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 440 " pdb=" ZN D 704 " pdb="ZN ZN D 704 " - pdb=" ND1 HIS D 448 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 420 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 451 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 417 " Number of angles added : 9 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2662 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 9 sheets defined 53.6% alpha, 6.0% beta 15 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 679 through 694 Processing helix chain 'A' and resid 699 through 711 Processing helix chain 'A' and resid 715 through 725 Processing helix chain 'A' and resid 759 through 764 removed outlier: 3.733A pdb=" N PHE A 764 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 778 Processing helix chain 'A' and resid 785 through 790 removed outlier: 3.799A pdb=" N ALA A 789 " --> pdb=" O HIS A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 839 removed outlier: 3.590A pdb=" N LYS A 837 " --> pdb=" O THR A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 875 through 885 removed outlier: 3.639A pdb=" N ASP A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 921 Processing helix chain 'A' and resid 923 through 928 Processing helix chain 'A' and resid 930 through 935 removed outlier: 3.840A pdb=" N THR A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 943 removed outlier: 3.811A pdb=" N LYS A 941 " --> pdb=" O GLN A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 960 removed outlier: 3.727A pdb=" N LEU A 948 " --> pdb=" O THR A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 999 removed outlier: 4.039A pdb=" N TYR A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1022 removed outlier: 4.180A pdb=" N GLU A1008 " --> pdb=" O ASN A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1031 Processing helix chain 'A' and resid 1141 through 1164 removed outlier: 3.993A pdb=" N MET A1164 " --> pdb=" O GLU A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1174 Processing helix chain 'A' and resid 1181 through 1186 Processing helix chain 'A' and resid 1202 through 1217 Processing helix chain 'A' and resid 1220 through 1233 removed outlier: 3.524A pdb=" N PHE A1224 " --> pdb=" O GLU A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1240 removed outlier: 3.698A pdb=" N LEU A1239 " --> pdb=" O ALA A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1258 Processing helix chain 'A' and resid 1259 through 1276 removed outlier: 3.647A pdb=" N SER A1276 " --> pdb=" O ASP A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1294 removed outlier: 3.550A pdb=" N TYR A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 54 removed outlier: 3.875A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.632A pdb=" N LYS B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 79 through 87 Processing helix chain 'B' and resid 98 through 105 removed outlier: 4.183A pdb=" N VAL B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 137 Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.558A pdb=" N LEU B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 removed outlier: 3.817A pdb=" N PHE B 197 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 243 through 262 removed outlier: 3.995A pdb=" N SER B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 272 through 276 removed outlier: 4.003A pdb=" N SER B 275 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 300 removed outlier: 4.006A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 330 removed outlier: 4.110A pdb=" N ARG B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 348 removed outlier: 4.155A pdb=" N GLY B 348 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 381 Processing helix chain 'C' and resid 225 through 241 Processing helix chain 'C' and resid 253 through 267 removed outlier: 3.630A pdb=" N GLN C 267 " --> pdb=" O HIS C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 297 removed outlier: 3.620A pdb=" N LEU C 278 " --> pdb=" O SER C 274 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER C 279 " --> pdb=" O GLN C 275 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 315 Processing helix chain 'C' and resid 321 through 325 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 369 removed outlier: 3.661A pdb=" N LEU C 354 " --> pdb=" O GLN C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 401 Processing helix chain 'D' and resid 120 through 127 Processing helix chain 'D' and resid 168 through 173 removed outlier: 4.013A pdb=" N LEU D 171 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU D 173 " --> pdb=" O PHE D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 Processing helix chain 'D' and resid 317 through 328 Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 403 through 407 Processing helix chain 'D' and resid 430 through 434 removed outlier: 3.635A pdb=" N SER D 434 " --> pdb=" O PRO D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 564 removed outlier: 3.595A pdb=" N LYS D 548 " --> pdb=" O GLU D 544 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP D 553 " --> pdb=" O TYR D 549 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS D 554 " --> pdb=" O ASP D 550 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN D 562 " --> pdb=" O SER D 558 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG D 564 " --> pdb=" O MET D 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 563 Processing sheet with id=AA1, first strand: chain 'A' and resid 975 through 978 removed outlier: 4.085A pdb=" N HIS A1311 " --> pdb=" O ASP A1306 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A1306 " --> pdb=" O HIS A1311 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 975 through 978 removed outlier: 4.085A pdb=" N HIS A1311 " --> pdb=" O ASP A1306 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A1306 " --> pdb=" O HIS A1311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 24 removed outlier: 6.414A pdb=" N TYR B 23 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA B 66 " --> pdb=" O TYR B 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 141 through 144 removed outlier: 7.349A pdb=" N VAL B 267 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL B 308 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 269 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 181 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B 180 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS B 206 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR B 182 " --> pdb=" O CYS B 206 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N PHE B 208 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASP B 184 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N LYS B 210 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU B 238 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N HIS B 209 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 245 through 246 Processing sheet with id=AA6, first strand: chain 'D' and resid 273 through 274 removed outlier: 3.683A pdb=" N PHE D 282 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 364 through 366 Processing sheet with id=AA8, first strand: chain 'D' and resid 473 through 476 Processing sheet with id=AA9, first strand: chain 'D' and resid 505 through 506 524 hydrogen bonds defined for protein. 1494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 1.46 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: 3254 1.33 - 1.45: 2422 1.45 - 1.57: 6626 1.57 - 1.69: 67 1.69 - 1.81: 100 Bond restraints: 12469 Sorted by residual: bond pdb=" C3' DT H -24 " pdb=" C2' DT H -24 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.31e+01 bond pdb=" C3' DC G 21 " pdb=" C2' DC G 21 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.69e+00 bond pdb=" C3' DT G 13 " pdb=" C2' DT G 13 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.20e+00 bond pdb=" C3' DG H -21 " pdb=" C2' DG H -21 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.75e+00 bond pdb=" C3' DC G 22 " pdb=" C2' DC G 22 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.54e+00 ... (remaining 12464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 16724 2.25 - 4.49: 201 4.49 - 6.74: 20 6.74 - 8.99: 3 8.99 - 11.24: 1 Bond angle restraints: 16949 Sorted by residual: angle pdb=" C ILE D 291 " pdb=" N ASP D 292 " pdb=" CA ASP D 292 " ideal model delta sigma weight residual 120.94 132.18 -11.24 1.90e+00 2.77e-01 3.50e+01 angle pdb=" CA PRO D 297 " pdb=" N PRO D 297 " pdb=" CD PRO D 297 " ideal model delta sigma weight residual 112.00 105.18 6.82 1.40e+00 5.10e-01 2.37e+01 angle pdb=" CA PRO D 119 " pdb=" N PRO D 119 " pdb=" CD PRO D 119 " ideal model delta sigma weight residual 112.00 105.18 6.82 1.40e+00 5.10e-01 2.37e+01 angle pdb=" N3 DT H -23 " pdb=" C4 DT H -23 " pdb=" O4 DT H -23 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT H -24 " pdb=" C4 DT H -24 " pdb=" O4 DT H -24 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 ... (remaining 16944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.50: 6757 26.50 - 53.00: 566 53.00 - 79.50: 79 79.50 - 106.00: 7 106.00 - 132.50: 1 Dihedral angle restraints: 7410 sinusoidal: 3293 harmonic: 4117 Sorted by residual: dihedral pdb=" CA GLN D 541 " pdb=" C GLN D 541 " pdb=" N ILE D 542 " pdb=" CA ILE D 542 " ideal model delta harmonic sigma weight residual -180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA PHE D 551 " pdb=" C PHE D 551 " pdb=" N PHE D 552 " pdb=" CA PHE D 552 " ideal model delta harmonic sigma weight residual -180.00 -157.48 -22.52 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA LYS B 153 " pdb=" C LYS B 153 " pdb=" N LYS B 154 " pdb=" CA LYS B 154 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 7407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1020 0.028 - 0.056: 513 0.056 - 0.084: 204 0.084 - 0.112: 75 0.112 - 0.140: 14 Chirality restraints: 1826 Sorted by residual: chirality pdb=" CA PRO A 786 " pdb=" N PRO A 786 " pdb=" C PRO A 786 " pdb=" CB PRO A 786 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA VAL D 108 " pdb=" N VAL D 108 " pdb=" C VAL D 108 " pdb=" CB VAL D 108 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA GLU B 252 " pdb=" N GLU B 252 " pdb=" C GLU B 252 " pdb=" CB GLU B 252 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 1823 not shown) Planarity restraints: 2046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 296 " 0.086 5.00e-02 4.00e+02 1.26e-01 2.54e+01 pdb=" N PRO D 297 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO D 297 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO D 297 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 118 " 0.084 5.00e-02 4.00e+02 1.23e-01 2.41e+01 pdb=" N PRO D 119 " -0.212 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 695 " 0.016 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" CG ASP A 695 " -0.058 2.00e-02 2.50e+03 pdb=" OD1 ASP A 695 " 0.021 2.00e-02 2.50e+03 pdb=" OD2 ASP A 695 " 0.020 2.00e-02 2.50e+03 ... (remaining 2043 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 169 2.63 - 3.20: 10848 3.20 - 3.76: 19091 3.76 - 4.33: 26267 4.33 - 4.90: 41890 Nonbonded interactions: 98265 Sorted by model distance: nonbonded pdb=" OD2 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.062 2.230 nonbonded pdb=" O ILE C 342 " pdb=" OG1 THR C 345 " model vdw 2.171 3.040 nonbonded pdb=" OG SER D 109 " pdb=" O LEU D 113 " model vdw 2.214 3.040 nonbonded pdb=" NE2 GLN D 510 " pdb=" O GLY D 513 " model vdw 2.224 3.120 nonbonded pdb=" O LYS D 321 " pdb=" OG SER D 324 " model vdw 2.232 3.040 ... (remaining 98260 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.680 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 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 : 0.003 0.090 12484 Z= 0.216 Angle : 0.620 11.236 16958 Z= 0.400 Chirality : 0.040 0.140 1826 Planarity : 0.006 0.126 2046 Dihedral : 18.253 132.505 4748 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.23 % Allowed : 20.34 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.23), residues: 1367 helix: 0.93 (0.21), residues: 645 sheet: -1.64 (0.57), residues: 87 loop : -2.30 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 868 TYR 0.016 0.001 TYR B 82 PHE 0.017 0.001 PHE A 668 TRP 0.011 0.001 TRP A1151 HIS 0.004 0.001 HIS A 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.22 (12469) covalent geometry : angle 0.61809 / 0.40 (16949) hydrogen bonds : bond 0.14249 / 16.09 ( 553) hydrogen bonds : angle 6.24707 / 6.59 ( 1572) metal coordination : bond 0.00386 / 0.42 ( 15) metal coordination : angle 2.14827 / 3.58 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 799 ARG cc_start: 0.6740 (mmm-85) cc_final: 0.5843 (tpp80) REVERT: A 913 ASN cc_start: 0.7249 (m110) cc_final: 0.6996 (m-40) REVERT: A 1156 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: D 438 MET cc_start: 0.7107 (tpt) cc_final: 0.6758 (tpt) outliers start: 3 outliers final: 1 residues processed: 112 average time/residue: 0.1191 time to fit residues: 18.9523 Evaluate side-chains 103 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain C residue 349 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 785 HIS C 275 GLN D 510 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.124994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.098080 restraints weight = 23532.596| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.18 r_work: 0.3335 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.0723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12484 Z= 0.183 Angle : 0.613 9.763 16958 Z= 0.332 Chirality : 0.043 0.174 1826 Planarity : 0.005 0.076 2046 Dihedral : 16.722 133.884 1877 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.74 % Allowed : 19.17 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.23), residues: 1367 helix: 0.97 (0.20), residues: 668 sheet: -1.68 (0.54), residues: 94 loop : -2.37 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 496 TYR 0.016 0.002 TYR B 313 PHE 0.020 0.002 PHE A1305 TRP 0.012 0.002 TRP A1151 HIS 0.006 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (12469) covalent geometry : angle 0.61092 / 0.33 (16949) hydrogen bonds : bond 0.05507 / 6.01 ( 553) hydrogen bonds : angle 4.93115 / 5.44 ( 1572) metal coordination : bond 0.00646 / 0.70 ( 15) metal coordination : angle 2.07272 / 3.41 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 695 ASP cc_start: 0.6938 (t0) cc_final: 0.6650 (t0) REVERT: A 868 ARG cc_start: 0.7802 (mmm160) cc_final: 0.7585 (mmm160) REVERT: C 237 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8087 (tm-30) REVERT: D 410 ASN cc_start: 0.7502 (m110) cc_final: 0.7146 (m-40) outliers start: 35 outliers final: 16 residues processed: 137 average time/residue: 0.1065 time to fit residues: 20.8369 Evaluate side-chains 117 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 561 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 10 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 70 optimal weight: 0.0670 chunk 9 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 785 HIS A 913 ASN C 369 HIS D 503 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.126626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.099840 restraints weight = 23588.171| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.16 r_work: 0.3371 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12484 Z= 0.121 Angle : 0.541 8.342 16958 Z= 0.296 Chirality : 0.041 0.154 1826 Planarity : 0.004 0.063 2046 Dihedral : 16.630 135.581 1872 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.43 % Allowed : 19.72 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.23), residues: 1367 helix: 1.18 (0.20), residues: 667 sheet: -1.29 (0.57), residues: 89 loop : -2.27 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1273 TYR 0.011 0.001 TYR B 313 PHE 0.010 0.001 PHE B 251 TRP 0.010 0.001 TRP A1151 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (12469) covalent geometry : angle 0.53914 / 0.30 (16949) hydrogen bonds : bond 0.04790 / 5.28 ( 553) hydrogen bonds : angle 4.55133 / 5.06 ( 1572) metal coordination : bond 0.00397 / 0.45 ( 15) metal coordination : angle 1.85210 / 3.09 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 669 PHE cc_start: 0.6893 (OUTLIER) cc_final: 0.6154 (t80) REVERT: A 695 ASP cc_start: 0.6810 (t70) cc_final: 0.6411 (t0) REVERT: A 913 ASN cc_start: 0.7131 (m-40) cc_final: 0.6761 (m-40) REVERT: B 170 ILE cc_start: 0.8243 (mt) cc_final: 0.7984 (mt) REVERT: D 410 ASN cc_start: 0.7520 (m110) cc_final: 0.7133 (m-40) outliers start: 31 outliers final: 17 residues processed: 137 average time/residue: 0.1211 time to fit residues: 23.8156 Evaluate side-chains 123 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain E residue 550 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 121 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 785 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.125645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.097875 restraints weight = 23331.607| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.16 r_work: 0.3368 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12484 Z= 0.148 Angle : 0.564 9.469 16958 Z= 0.304 Chirality : 0.041 0.160 1826 Planarity : 0.004 0.058 2046 Dihedral : 16.638 136.836 1872 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 3.76 % Allowed : 18.15 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.23), residues: 1367 helix: 1.19 (0.20), residues: 667 sheet: -1.21 (0.57), residues: 89 loop : -2.22 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 136 TYR 0.013 0.001 TYR B 313 PHE 0.015 0.001 PHE B 251 TRP 0.012 0.001 TRP A1151 HIS 0.006 0.001 HIS A 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (12469) covalent geometry : angle 0.56180 / 0.30 (16949) hydrogen bonds : bond 0.04820 / 5.29 ( 553) hydrogen bonds : angle 4.45366 / 4.97 ( 1572) metal coordination : bond 0.00541 / 0.58 ( 15) metal coordination : angle 1.98126 / 3.28 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 107 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 669 PHE cc_start: 0.7019 (OUTLIER) cc_final: 0.6226 (t80) REVERT: A 695 ASP cc_start: 0.6987 (t70) cc_final: 0.6565 (t0) REVERT: A 1156 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: B 95 GLU cc_start: 0.8065 (tt0) cc_final: 0.7637 (pt0) REVERT: C 237 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8323 (tm-30) REVERT: D 410 ASN cc_start: 0.7687 (m110) cc_final: 0.7457 (m-40) outliers start: 48 outliers final: 27 residues processed: 148 average time/residue: 0.1061 time to fit residues: 22.7772 Evaluate side-chains 132 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain E residue 550 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 60 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 0.0270 chunk 84 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 785 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.125892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.098926 restraints weight = 23502.086| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.17 r_work: 0.3354 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12484 Z= 0.136 Angle : 0.557 9.402 16958 Z= 0.301 Chirality : 0.041 0.156 1826 Planarity : 0.004 0.056 2046 Dihedral : 16.630 137.906 1872 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.05 % Allowed : 19.72 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.23), residues: 1367 helix: 1.21 (0.20), residues: 669 sheet: -1.26 (0.55), residues: 94 loop : -2.20 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 136 TYR 0.013 0.001 TYR B 313 PHE 0.013 0.001 PHE B 251 TRP 0.011 0.001 TRP A1151 HIS 0.005 0.001 HIS A 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (12469) covalent geometry : angle 0.55556 / 0.30 (16949) hydrogen bonds : bond 0.04712 / 5.18 ( 553) hydrogen bonds : angle 4.38037 / 4.96 ( 1572) metal coordination : bond 0.00504 / 0.52 ( 15) metal coordination : angle 1.89565 / 3.17 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 669 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.6161 (t80) REVERT: A 695 ASP cc_start: 0.6925 (t70) cc_final: 0.6456 (t0) REVERT: A 1156 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: B 95 GLU cc_start: 0.7875 (tt0) cc_final: 0.7501 (pt0) REVERT: C 237 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8274 (tm-30) REVERT: D 410 ASN cc_start: 0.7508 (m110) cc_final: 0.7122 (m-40) outliers start: 39 outliers final: 31 residues processed: 140 average time/residue: 0.0929 time to fit residues: 19.3969 Evaluate side-chains 135 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 973 SER Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain E residue 550 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 119 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 0.0020 chunk 129 optimal weight: 1.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 785 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.126443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.099310 restraints weight = 23296.591| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.26 r_work: 0.3355 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12484 Z= 0.126 Angle : 0.543 8.856 16958 Z= 0.294 Chirality : 0.041 0.156 1826 Planarity : 0.004 0.052 2046 Dihedral : 16.596 138.858 1872 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.44 % Allowed : 19.33 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.23), residues: 1367 helix: 1.27 (0.20), residues: 669 sheet: -1.16 (0.55), residues: 94 loop : -2.17 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.013 0.001 TYR B 313 PHE 0.013 0.001 PHE B 251 TRP 0.011 0.001 TRP A1151 HIS 0.004 0.001 HIS A 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (12469) covalent geometry : angle 0.54121 / 0.29 (16949) hydrogen bonds : bond 0.04543 / 5.00 ( 553) hydrogen bonds : angle 4.28324 / 4.84 ( 1572) metal coordination : bond 0.00474 / 0.49 ( 15) metal coordination : angle 1.83556 / 3.08 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 665 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.6006 (mp0) REVERT: A 669 PHE cc_start: 0.6889 (OUTLIER) cc_final: 0.6122 (t80) REVERT: A 695 ASP cc_start: 0.6955 (t70) cc_final: 0.6494 (t0) REVERT: A 913 ASN cc_start: 0.7270 (m-40) cc_final: 0.6847 (m-40) REVERT: A 1156 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7441 (tt0) REVERT: B 95 GLU cc_start: 0.7895 (tt0) cc_final: 0.7520 (pt0) REVERT: C 237 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8282 (tm-30) REVERT: D 410 ASN cc_start: 0.7483 (m110) cc_final: 0.7095 (m-40) REVERT: D 491 VAL cc_start: 0.6910 (t) cc_final: 0.6710 (p) outliers start: 44 outliers final: 32 residues processed: 143 average time/residue: 0.1008 time to fit residues: 21.5310 Evaluate side-chains 140 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 973 SER Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain E residue 550 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 109 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 128 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 785 HIS ** D 283 HIS ** 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 = 0.3932 r_free = 0.3932 target = 0.125133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.098130 restraints weight = 23224.343| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.18 r_work: 0.3329 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12484 Z= 0.173 Angle : 0.594 11.082 16958 Z= 0.316 Chirality : 0.042 0.162 1826 Planarity : 0.005 0.056 2046 Dihedral : 16.649 139.219 1872 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.76 % Allowed : 19.80 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.23), residues: 1367 helix: 1.20 (0.20), residues: 670 sheet: -1.28 (0.55), residues: 94 loop : -2.18 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 320 TYR 0.017 0.002 TYR B 313 PHE 0.017 0.002 PHE B 251 TRP 0.012 0.001 TRP A1151 HIS 0.006 0.001 HIS A 785 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (12469) covalent geometry : angle 0.59203 / 0.32 (16949) hydrogen bonds : bond 0.04878 / 5.33 ( 553) hydrogen bonds : angle 4.38608 / 4.96 ( 1572) metal coordination : bond 0.00734 / 0.75 ( 15) metal coordination : angle 2.03326 / 3.38 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 104 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 665 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.5916 (mp0) REVERT: A 669 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.6153 (t80) REVERT: A 695 ASP cc_start: 0.7133 (t70) cc_final: 0.6696 (t0) REVERT: A 1156 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7482 (tt0) REVERT: B 95 GLU cc_start: 0.7871 (tt0) cc_final: 0.7518 (pt0) REVERT: D 410 ASN cc_start: 0.7566 (m110) cc_final: 0.7206 (m-40) outliers start: 48 outliers final: 39 residues processed: 143 average time/residue: 0.1012 time to fit residues: 21.3290 Evaluate side-chains 143 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 101 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 973 SER Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain E residue 550 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 120 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 111 optimal weight: 0.0870 chunk 77 optimal weight: 0.8980 chunk 113 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 39 optimal weight: 0.0970 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 785 HIS ** B 38 HIS ** 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 = 0.3969 r_free = 0.3969 target = 0.127707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.101046 restraints weight = 23104.686| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.15 r_work: 0.3378 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12484 Z= 0.110 Angle : 0.532 7.155 16958 Z= 0.288 Chirality : 0.040 0.163 1826 Planarity : 0.004 0.048 2046 Dihedral : 16.530 139.531 1872 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.27 % Allowed : 21.44 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.23), residues: 1367 helix: 1.40 (0.20), residues: 668 sheet: -0.99 (0.55), residues: 90 loop : -2.09 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.009 0.001 TYR B 313 PHE 0.010 0.001 PHE D 552 TRP 0.010 0.001 TRP A1151 HIS 0.003 0.001 HIS A1252 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 (12469) covalent geometry : angle 0.53050 / 0.29 (16949) hydrogen bonds : bond 0.04216 / 4.68 ( 553) hydrogen bonds : angle 4.14887 / 4.71 ( 1572) metal coordination : bond 0.00326 / 0.39 ( 15) metal coordination : angle 1.87884 / 3.13 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 669 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.6170 (t80) REVERT: A 695 ASP cc_start: 0.6994 (t70) cc_final: 0.6566 (t0) REVERT: A 773 MET cc_start: 0.5978 (ttt) cc_final: 0.5559 (ttt) REVERT: A 1156 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: B 95 GLU cc_start: 0.7900 (tt0) cc_final: 0.7549 (pt0) REVERT: D 410 ASN cc_start: 0.7434 (m110) cc_final: 0.7010 (m-40) outliers start: 29 outliers final: 22 residues processed: 138 average time/residue: 0.0958 time to fit residues: 19.6132 Evaluate side-chains 132 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain E residue 550 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.0370 chunk 70 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 0.0040 chunk 110 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 13 optimal weight: 0.0970 overall best weight: 0.3870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.127809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.100758 restraints weight = 23115.797| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.16 r_work: 0.3391 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12484 Z= 0.110 Angle : 0.529 7.196 16958 Z= 0.286 Chirality : 0.040 0.158 1826 Planarity : 0.004 0.047 2046 Dihedral : 16.470 139.829 1872 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.35 % Allowed : 21.67 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.23), residues: 1367 helix: 1.45 (0.20), residues: 668 sheet: -0.97 (0.56), residues: 90 loop : -2.00 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.026 0.001 TYR A1204 PHE 0.011 0.001 PHE A1305 TRP 0.009 0.001 TRP A 719 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (12469) covalent geometry : angle 0.52753 / 0.29 (16949) hydrogen bonds : bond 0.04150 / 4.59 ( 553) hydrogen bonds : angle 4.10170 / 4.69 ( 1572) metal coordination : bond 0.00342 / 0.36 ( 15) metal coordination : angle 1.74194 / 2.90 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 669 PHE cc_start: 0.6812 (OUTLIER) cc_final: 0.6125 (t80) REVERT: A 695 ASP cc_start: 0.6987 (t70) cc_final: 0.6550 (t0) REVERT: A 773 MET cc_start: 0.6022 (ttt) cc_final: 0.5597 (ttt) REVERT: A 1156 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7402 (tt0) REVERT: B 95 GLU cc_start: 0.7902 (tt0) cc_final: 0.7537 (pt0) REVERT: D 410 ASN cc_start: 0.7411 (m110) cc_final: 0.6999 (m-40) outliers start: 30 outliers final: 26 residues processed: 137 average time/residue: 0.1051 time to fit residues: 21.2257 Evaluate side-chains 137 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 973 SER Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain E residue 550 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 2 optimal weight: 0.0470 chunk 34 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.127760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.100860 restraints weight = 23340.482| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.19 r_work: 0.3384 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12484 Z= 0.115 Angle : 0.537 7.690 16958 Z= 0.292 Chirality : 0.040 0.163 1826 Planarity : 0.004 0.047 2046 Dihedral : 16.441 139.833 1872 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.43 % Allowed : 21.60 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.23), residues: 1367 helix: 1.47 (0.20), residues: 671 sheet: -1.02 (0.55), residues: 94 loop : -1.95 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.023 0.001 TYR A1204 PHE 0.009 0.001 PHE B 251 TRP 0.009 0.001 TRP A1151 HIS 0.004 0.001 HIS A 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (12469) covalent geometry : angle 0.53603 / 0.29 (16949) hydrogen bonds : bond 0.04147 / 4.59 ( 553) hydrogen bonds : angle 4.07987 / 4.67 ( 1572) metal coordination : bond 0.00380 / 0.39 ( 15) metal coordination : angle 1.66878 / 2.79 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 669 PHE cc_start: 0.6806 (OUTLIER) cc_final: 0.6121 (t80) REVERT: A 695 ASP cc_start: 0.7023 (t70) cc_final: 0.6602 (t0) REVERT: A 773 MET cc_start: 0.5988 (ttt) cc_final: 0.5569 (ttt) REVERT: A 1156 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7384 (tt0) REVERT: A 1190 GLN cc_start: 0.7080 (tp40) cc_final: 0.6750 (tp40) REVERT: B 95 GLU cc_start: 0.7948 (tt0) cc_final: 0.7593 (pt0) REVERT: C 349 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7502 (tt) REVERT: D 410 ASN cc_start: 0.7410 (m110) cc_final: 0.6992 (m-40) REVERT: D 544 GLU cc_start: 0.7321 (tm-30) cc_final: 0.7092 (tm-30) REVERT: D 560 MET cc_start: 0.6804 (mmm) cc_final: 0.5931 (tpt) outliers start: 31 outliers final: 26 residues processed: 135 average time/residue: 0.1042 time to fit residues: 20.9039 Evaluate side-chains 139 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 973 SER Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain E residue 550 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 56 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 120 optimal weight: 0.0070 chunk 10 optimal weight: 5.9990 chunk 70 optimal weight: 0.0370 chunk 12 optimal weight: 0.0980 chunk 48 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 HIS ** C 350 GLN ** 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 = 0.3982 r_free = 0.3982 target = 0.128557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.101588 restraints weight = 23166.075| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.15 r_work: 0.3401 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12484 Z= 0.106 Angle : 0.529 13.184 16958 Z= 0.284 Chirality : 0.040 0.167 1826 Planarity : 0.004 0.047 2046 Dihedral : 16.375 139.720 1872 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.03 % Allowed : 22.07 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.23), residues: 1367 helix: 1.54 (0.20), residues: 668 sheet: -0.88 (0.56), residues: 90 loop : -1.90 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.020 0.001 TYR A1204 PHE 0.014 0.001 PHE A1305 TRP 0.008 0.001 TRP A 719 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 (12469) covalent geometry : angle 0.52729 / 0.28 (16949) hydrogen bonds : bond 0.03982 / 4.42 ( 553) hydrogen bonds : angle 4.00793 / 4.59 ( 1572) metal coordination : bond 0.00292 / 0.32 ( 15) metal coordination : angle 1.66292 / 2.77 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2456.48 seconds wall clock time: 43 minutes 19.73 seconds (2599.73 seconds total)