Starting phenix.real_space_refine on Tue Mar 3 22:40:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oti_13060/03_2026/7oti_13060.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oti_13060/03_2026/7oti_13060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oti_13060/03_2026/7oti_13060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oti_13060/03_2026/7oti_13060.map" model { file = "/net/cci-nas-00/data/ceres_data/7oti_13060/03_2026/7oti_13060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oti_13060/03_2026/7oti_13060.cif" } resolution = 4.2 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= 0.007 sd= 0.210 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 5895 2.51 5 N 1552 2.21 5 O 1686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9171 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1182, 9171 Classifications: {'peptide': 1182} Link IDs: {'PTRANS': 29, 'TRANS': 1152} Chain breaks: 1 Time building chain proxies: 1.93, per 1000 atoms: 0.21 Number of scatterers: 9171 At special positions: 0 Unit cell: (120.988, 109.515, 112.644, 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 38 16.00 O 1686 8.00 N 1552 7.00 C 5895 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: 0.70 Conformation dependent library (CDL) restraints added in 357.6 milliseconds 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 68.1% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 34 through 41 removed outlier: 3.881A pdb=" N PHE A 39 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A 40 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 86 removed outlier: 3.727A pdb=" N LEU A 48 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET A 50 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) Proline residue: A 65 - end of helix removed outlier: 3.533A pdb=" N THR A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 134 removed outlier: 4.158A pdb=" N ARG A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE A 100 " --> pdb=" O LYS A 96 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 111 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 122 " --> pdb=" O GLY A 118 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 152 removed outlier: 5.425A pdb=" N HIS A 149 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.793A pdb=" N ASP A 160 " --> pdb=" O ILE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 181 removed outlier: 4.108A pdb=" N ASP A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 207 removed outlier: 4.149A pdb=" N GLY A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 256 removed outlier: 3.877A pdb=" N THR A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Proline residue: A 219 - end of helix removed outlier: 4.162A pdb=" N LYS A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LYS A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 264 through 269 removed outlier: 3.827A pdb=" N GLU A 269 " --> pdb=" O GLN A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 315 removed outlier: 3.995A pdb=" N ASN A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 277 " --> pdb=" O TYR A 273 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LYS A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 363 removed outlier: 3.771A pdb=" N PHE A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Proline residue: A 346 - end of helix removed outlier: 3.847A pdb=" N GLY A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS A 363 " --> pdb=" O TYR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 436 removed outlier: 4.156A pdb=" N VAL A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 505 through 511 removed outlier: 3.532A pdb=" N ILE A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 528 through 542 removed outlier: 3.811A pdb=" N ILE A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 573 removed outlier: 4.079A pdb=" N LYS A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 590 removed outlier: 3.710A pdb=" N VAL A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 removed outlier: 3.637A pdb=" N ARG A 613 " --> pdb=" O ASP A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 623 Processing helix chain 'A' and resid 694 through 699 removed outlier: 3.619A pdb=" N LEU A 699 " --> pdb=" O ARG A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 704 removed outlier: 3.649A pdb=" N GLU A 703 " --> pdb=" O LEU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 737 removed outlier: 3.953A pdb=" N GLN A 721 " --> pdb=" O ASN A 717 " (cutoff:3.500A) Proline residue: A 722 - end of helix removed outlier: 4.078A pdb=" N SER A 725 " --> pdb=" O GLN A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 757 removed outlier: 3.529A pdb=" N GLN A 746 " --> pdb=" O GLU A 742 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 749 " --> pdb=" O ARG A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 793 removed outlier: 4.248A pdb=" N LYS A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG A 785 " --> pdb=" O THR A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 838 removed outlier: 3.652A pdb=" N THR A 811 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ALA A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY A 826 " --> pdb=" O LYS A 822 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU A 829 " --> pdb=" O THR A 825 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 832 " --> pdb=" O ARG A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 846 removed outlier: 3.815A pdb=" N ILE A 843 " --> pdb=" O LEU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 889 Proline residue: A 862 - end of helix removed outlier: 4.117A pdb=" N LYS A 873 " --> pdb=" O VAL A 869 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A 884 " --> pdb=" O LEU A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 895 Processing helix chain 'A' and resid 899 through 905 removed outlier: 3.830A pdb=" N VAL A 903 " --> pdb=" O PHE A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 920 removed outlier: 4.155A pdb=" N GLN A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 918 " --> pdb=" O THR A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 955 removed outlier: 3.929A pdb=" N MET A 945 " --> pdb=" O THR A 941 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR A 946 " --> pdb=" O GLN A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 removed outlier: 3.740A pdb=" N GLN A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1010 removed outlier: 3.716A pdb=" N VAL A 973 " --> pdb=" O ASN A 969 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N SER A 989 " --> pdb=" O GLY A 985 " (cutoff:3.500A) Proline residue: A 992 - end of helix removed outlier: 3.613A pdb=" N THR A 998 " --> pdb=" O TYR A 994 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 999 " --> pdb=" O ALA A 995 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS A1003 " --> pdb=" O VAL A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1027 Processing helix chain 'A' and resid 1042 through 1046 Processing helix chain 'A' and resid 1071 through 1080 removed outlier: 4.459A pdb=" N LEU A1078 " --> pdb=" O THR A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1100 Processing helix chain 'A' and resid 1101 through 1106 Processing helix chain 'A' and resid 1122 through 1128 removed outlier: 3.939A pdb=" N ALA A1128 " --> pdb=" O ALA A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1148 Processing helix chain 'A' and resid 1151 through 1156 Processing helix chain 'A' and resid 1159 through 1163 Processing helix chain 'A' and resid 1173 through 1187 Processing helix chain 'A' and resid 1204 through 1215 Processing helix chain 'A' and resid 1229 through 1235 removed outlier: 3.756A pdb=" N ILE A1233 " --> pdb=" O ARG A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1257 Processing helix chain 'A' and resid 1261 through 1269 removed outlier: 5.395A pdb=" N VAL A1267 " --> pdb=" O TYR A1263 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 409 removed outlier: 3.890A pdb=" N GLY A 408 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE A 393 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE A 393 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP A 444 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 579 through 580 removed outlier: 6.409A pdb=" N ALA A 420 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE A 597 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N VAL A 422 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A 604 " --> pdb=" O GLY A 596 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASP A 598 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ILE A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 466 through 468 Processing sheet with id=AA4, first strand: chain 'A' and resid 1049 through 1055 removed outlier: 6.264A pdb=" N GLN A1050 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL A1037 " --> pdb=" O GLN A1050 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU A1052 " --> pdb=" O GLY A1035 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL A1036 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA A1087 " --> pdb=" O VAL A1036 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1192 through 1195 removed outlier: 6.573A pdb=" N LEU A1193 " --> pdb=" O ILE A1224 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLN A1060 " --> pdb=" O CYS A1223 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL A1225 " --> pdb=" O GLN A1060 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A1062 " --> pdb=" O VAL A1225 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR A1061 " --> pdb=" O LEU A1238 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VAL A1240 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA A1063 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE A1242 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL A1065 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A1249 " --> pdb=" O VAL A1241 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLN A1243 " --> pdb=" O VAL A1247 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N VAL A1247 " --> pdb=" O GLN A1243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1120 through 1121 removed outlier: 4.239A pdb=" N GLY A1166 " --> pdb=" O CYS A1121 " (cutoff:3.500A) 530 hydrogen bonds defined for protein. 1524 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: 1.62 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1817 1.33 - 1.45: 2112 1.45 - 1.58: 5341 1.58 - 1.70: 0 1.70 - 1.82: 69 Bond restraints: 9339 Sorted by residual: bond pdb=" CA PRO A 740 " pdb=" C PRO A 740 " ideal model delta sigma weight residual 1.517 1.549 -0.032 9.30e-03 1.16e+04 1.18e+01 bond pdb=" CA PRO A 689 " pdb=" C PRO A 689 " ideal model delta sigma weight residual 1.517 1.548 -0.031 9.30e-03 1.16e+04 1.13e+01 bond pdb=" CZ ARG A1229 " pdb=" NH2 ARG A1229 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.96e+00 bond pdb=" CZ ARG A 783 " pdb=" NH2 ARG A 783 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.51e+00 bond pdb=" CZ ARG A1218 " pdb=" NH2 ARG A1218 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.46e+00 ... (remaining 9334 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 9780 2.34 - 4.69: 2539 4.69 - 7.03: 277 7.03 - 9.38: 25 9.38 - 11.72: 5 Bond angle restraints: 12626 Sorted by residual: angle pdb=" N PRO A 689 " pdb=" CA PRO A 689 " pdb=" C PRO A 689 " ideal model delta sigma weight residual 110.70 122.42 -11.72 1.22e+00 6.72e-01 9.23e+01 angle pdb=" CA PHE A 979 " pdb=" CB PHE A 979 " pdb=" CG PHE A 979 " ideal model delta sigma weight residual 113.80 122.00 -8.20 1.00e+00 1.00e+00 6.72e+01 angle pdb=" N PRO A 740 " pdb=" CA PRO A 740 " pdb=" C PRO A 740 " ideal model delta sigma weight residual 110.70 119.98 -9.28 1.22e+00 6.72e-01 5.78e+01 angle pdb=" CA ASP A 558 " pdb=" CB ASP A 558 " pdb=" CG ASP A 558 " ideal model delta sigma weight residual 112.60 119.77 -7.17 1.00e+00 1.00e+00 5.14e+01 angle pdb=" CA PHE A 39 " pdb=" CB PHE A 39 " pdb=" CG PHE A 39 " ideal model delta sigma weight residual 113.80 119.83 -6.03 1.00e+00 1.00e+00 3.64e+01 ... (remaining 12621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.50: 5040 19.50 - 38.99: 389 38.99 - 58.49: 93 58.49 - 77.98: 28 77.98 - 97.48: 18 Dihedral angle restraints: 5568 sinusoidal: 2178 harmonic: 3390 Sorted by residual: dihedral pdb=" CA VAL A 474 " pdb=" C VAL A 474 " pdb=" N LEU A 475 " pdb=" CA LEU A 475 " ideal model delta harmonic sigma weight residual 180.00 142.13 37.87 0 5.00e+00 4.00e-02 5.74e+01 dihedral pdb=" CA ILE A 384 " pdb=" C ILE A 384 " pdb=" N GLN A 385 " pdb=" CA GLN A 385 " ideal model delta harmonic sigma weight residual 180.00 143.38 36.62 0 5.00e+00 4.00e-02 5.36e+01 dihedral pdb=" CA LEU A1092 " pdb=" C LEU A1092 " pdb=" N ASP A1093 " pdb=" CA ASP A1093 " ideal model delta harmonic sigma weight residual 180.00 143.68 36.32 0 5.00e+00 4.00e-02 5.28e+01 ... (remaining 5565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1079 0.108 - 0.215: 310 0.215 - 0.323: 50 0.323 - 0.430: 13 0.430 - 0.538: 4 Chirality restraints: 1456 Sorted by residual: chirality pdb=" CA THR A1204 " pdb=" N THR A1204 " pdb=" C THR A1204 " pdb=" CB THR A1204 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.54 2.00e-01 2.50e+01 7.23e+00 chirality pdb=" CA ASP A 517 " pdb=" N ASP A 517 " pdb=" C ASP A 517 " pdb=" CB ASP A 517 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.45e+00 chirality pdb=" CA LYS A1010 " pdb=" N LYS A1010 " pdb=" C LYS A1010 " pdb=" CB LYS A1010 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.82e+00 ... (remaining 1453 not shown) Planarity restraints: 1605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 359 " 0.188 2.00e-02 2.50e+03 1.12e-01 2.50e+02 pdb=" CG TYR A 359 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 359 " -0.080 2.00e-02 2.50e+03 pdb=" CD2 TYR A 359 " -0.093 2.00e-02 2.50e+03 pdb=" CE1 TYR A 359 " -0.086 2.00e-02 2.50e+03 pdb=" CE2 TYR A 359 " -0.072 2.00e-02 2.50e+03 pdb=" CZ TYR A 359 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 359 " 0.189 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1083 " -0.186 2.00e-02 2.50e+03 1.07e-01 2.31e+02 pdb=" CG TYR A1083 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A1083 " 0.090 2.00e-02 2.50e+03 pdb=" CD2 TYR A1083 " 0.078 2.00e-02 2.50e+03 pdb=" CE1 TYR A1083 " 0.065 2.00e-02 2.50e+03 pdb=" CE2 TYR A1083 " 0.077 2.00e-02 2.50e+03 pdb=" CZ TYR A1083 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR A1083 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 243 " -0.187 2.00e-02 2.50e+03 9.75e-02 1.90e+02 pdb=" CG TYR A 243 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 TYR A 243 " 0.080 2.00e-02 2.50e+03 pdb=" CD2 TYR A 243 " 0.090 2.00e-02 2.50e+03 pdb=" CE1 TYR A 243 " 0.048 2.00e-02 2.50e+03 pdb=" CE2 TYR A 243 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 243 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 243 " -0.131 2.00e-02 2.50e+03 ... (remaining 1602 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 4404 2.99 - 3.46: 10662 3.46 - 3.94: 15991 3.94 - 4.42: 17608 4.42 - 4.90: 27951 Nonbonded interactions: 76616 Sorted by model distance: nonbonded pdb=" OD1 ASP A 687 " pdb=" OG SER A1000 " model vdw 2.507 3.040 nonbonded pdb=" OG SER A1173 " pdb=" OD2 ASP A1203 " model vdw 2.525 3.040 nonbonded pdb=" OG SER A 88 " pdb=" OD2 ASP A 95 " model vdw 2.531 3.040 nonbonded pdb=" OD2 ASP A 802 " pdb=" OG1 THR A1042 " model vdw 2.536 3.040 nonbonded pdb=" OE2 GLU A 155 " pdb=" OG SER A 375 " model vdw 2.538 3.040 ... (remaining 76611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.330 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2534 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 : 0.014 0.041 9339 Z= 0.851 Angle : 1.994 11.720 12626 Z= 1.325 Chirality : 0.104 0.538 1456 Planarity : 0.018 0.181 1605 Dihedral : 16.952 97.478 3394 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 1.36 % Allowed : 10.78 % Favored : 87.86 % Rotamer: Outliers : 4.71 % Allowed : 9.63 % Favored : 85.66 % Cbeta Deviations : 1.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.52 % 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: -3.63 (0.20), residues: 1178 helix: -1.84 (0.16), residues: 743 sheet: -3.47 (0.59), residues: 43 loop : -3.14 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.003 ARG A1164 TYR 0.189 0.029 TYR A 359 PHE 0.069 0.013 PHE A 979 TRP 0.130 0.023 TRP A 132 HIS 0.027 0.005 HIS A1003 Details of bonding type rmsd covalent geometry : bond 0.01426 ( 9339) covalent geometry : angle 1.99357 (12626) hydrogen bonds : bond 0.19006 ( 530) hydrogen bonds : angle 8.25543 ( 1524) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 267 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.7039 (mt) cc_final: 0.6590 (mm) REVERT: A 108 THR cc_start: 0.1207 (m) cc_final: 0.0774 (m) REVERT: A 175 VAL cc_start: 0.3435 (m) cc_final: 0.2843 (m) REVERT: A 512 LEU cc_start: -0.0349 (mt) cc_final: -0.0669 (mt) REVERT: A 542 VAL cc_start: -0.1631 (OUTLIER) cc_final: -0.1980 (p) REVERT: A 574 GLU cc_start: -0.1998 (OUTLIER) cc_final: -0.3389 (mm-30) REVERT: A 926 ASN cc_start: 0.3775 (t0) cc_final: 0.3128 (t0) REVERT: A 941 THR cc_start: 0.5614 (m) cc_final: 0.5232 (m) REVERT: A 978 VAL cc_start: 0.6527 (t) cc_final: 0.6271 (t) REVERT: A 1026 MET cc_start: 0.1289 (mtt) cc_final: 0.0618 (ppp) REVERT: A 1078 LEU cc_start: 0.1434 (mt) cc_final: 0.0897 (mp) REVERT: A 1139 GLU cc_start: 0.4120 (mp0) cc_final: 0.2271 (pp20) outliers start: 46 outliers final: 7 residues processed: 302 average time/residue: 0.1096 time to fit residues: 43.3645 Evaluate side-chains 161 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.0570 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 191 GLN A 347 ASN A 424 ASN A 437 GLN A 504 ASN A 608 HIS ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 GLN ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.188115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.170574 restraints weight = 35721.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.173666 restraints weight = 26262.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.175833 restraints weight = 19792.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.177406 restraints weight = 15870.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.178565 restraints weight = 13400.045| |-----------------------------------------------------------------------------| r_work (final): 0.4772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4666 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9339 Z= 0.193 Angle : 0.835 10.386 12626 Z= 0.454 Chirality : 0.047 0.177 1456 Planarity : 0.006 0.048 1605 Dihedral : 7.082 41.240 1267 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.05 % Favored : 92.44 % Rotamer: Outliers : 0.61 % Allowed : 5.12 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.09 % 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: -2.05 (0.23), residues: 1178 helix: -0.52 (0.18), residues: 744 sheet: -2.85 (0.50), residues: 65 loop : -2.65 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 785 TYR 0.018 0.002 TYR A1040 PHE 0.041 0.003 PHE A 196 TRP 0.014 0.002 TRP A 694 HIS 0.007 0.002 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9339) covalent geometry : angle 0.83498 (12626) hydrogen bonds : bond 0.06323 ( 530) hydrogen bonds : angle 5.60726 ( 1524) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 200 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.5064 (t80) cc_final: 0.4716 (m-80) REVERT: A 49 TYR cc_start: 0.6805 (m-80) cc_final: 0.6435 (m-10) REVERT: A 102 LYS cc_start: 0.7225 (tptm) cc_final: 0.6881 (mttt) REVERT: A 103 LEU cc_start: 0.7552 (mt) cc_final: 0.7342 (mt) REVERT: A 143 ILE cc_start: 0.7530 (mm) cc_final: 0.5936 (mm) REVERT: A 152 MET cc_start: 0.3914 (ptt) cc_final: 0.3051 (ptt) REVERT: A 175 VAL cc_start: 0.6218 (m) cc_final: 0.5389 (m) REVERT: A 186 ILE cc_start: 0.8462 (pt) cc_final: 0.7667 (pt) REVERT: A 188 MET cc_start: 0.8398 (mmm) cc_final: 0.8148 (mmp) REVERT: A 812 THR cc_start: 0.8442 (p) cc_final: 0.8218 (p) REVERT: A 872 MET cc_start: 0.8082 (mmp) cc_final: 0.7879 (mmp) REVERT: A 930 LYS cc_start: 0.8877 (ttpt) cc_final: 0.8163 (tttt) REVERT: A 982 MET cc_start: 0.5661 (mmm) cc_final: 0.5431 (tpt) REVERT: A 1139 GLU cc_start: 0.5553 (mp0) cc_final: 0.3948 (pp20) outliers start: 6 outliers final: 0 residues processed: 206 average time/residue: 0.1117 time to fit residues: 30.7446 Evaluate side-chains 137 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 92 optimal weight: 10.0000 chunk 87 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN A 275 ASN A 437 GLN A 820 GLN ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1228 HIS A1234 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.184633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.168528 restraints weight = 37268.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.171278 restraints weight = 27651.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.173397 restraints weight = 20892.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.174600 restraints weight = 16751.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.175604 restraints weight = 14350.325| |-----------------------------------------------------------------------------| r_work (final): 0.4739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4809 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9339 Z= 0.168 Angle : 0.764 9.721 12626 Z= 0.411 Chirality : 0.045 0.165 1456 Planarity : 0.005 0.049 1605 Dihedral : 6.397 34.653 1267 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.79 % Favored : 92.70 % Rotamer: Outliers : 0.20 % Allowed : 4.41 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.65 (0.23), residues: 1178 helix: -0.21 (0.18), residues: 737 sheet: -2.56 (0.53), residues: 66 loop : -2.47 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 828 TYR 0.018 0.002 TYR A1040 PHE 0.057 0.003 PHE A 148 TRP 0.032 0.002 TRP A 132 HIS 0.013 0.002 HIS A1191 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9339) covalent geometry : angle 0.76391 (12626) hydrogen bonds : bond 0.05542 ( 530) hydrogen bonds : angle 5.18150 ( 1524) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 189 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.5130 (t80) cc_final: 0.4893 (m-80) REVERT: A 99 MET cc_start: 0.0470 (mmm) cc_final: -0.0049 (mpp) REVERT: A 152 MET cc_start: 0.4282 (ptt) cc_final: 0.3326 (ptt) REVERT: A 461 TYR cc_start: 0.4406 (t80) cc_final: 0.4008 (t80) REVERT: A 812 THR cc_start: 0.8578 (p) cc_final: 0.8317 (p) REVERT: A 874 MET cc_start: 0.8501 (tpp) cc_final: 0.8299 (tpp) REVERT: A 883 LYS cc_start: 0.8778 (ptpp) cc_final: 0.8563 (ptpt) REVERT: A 891 LYS cc_start: 0.8365 (mmmt) cc_final: 0.7166 (mttm) REVERT: A 897 ILE cc_start: 0.7525 (pt) cc_final: 0.7214 (pt) REVERT: A 930 LYS cc_start: 0.8917 (ttmt) cc_final: 0.8523 (tttt) REVERT: A 944 MET cc_start: 0.8152 (mmm) cc_final: 0.7270 (mtp) REVERT: A 1026 MET cc_start: 0.0634 (mpp) cc_final: -0.1087 (ppp) REVERT: A 1162 ASN cc_start: 0.7445 (m-40) cc_final: 0.7105 (p0) outliers start: 2 outliers final: 0 residues processed: 190 average time/residue: 0.0964 time to fit residues: 24.8241 Evaluate side-chains 128 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 78 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 GLN A1020 GLN ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.182146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.164454 restraints weight = 40186.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.167578 restraints weight = 29333.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.169675 restraints weight = 22442.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.171001 restraints weight = 18111.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.172070 restraints weight = 15559.604| |-----------------------------------------------------------------------------| r_work (final): 0.4694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4951 moved from start: 0.6624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9339 Z= 0.149 Angle : 0.717 9.951 12626 Z= 0.383 Chirality : 0.044 0.169 1456 Planarity : 0.005 0.052 1605 Dihedral : 5.926 34.081 1267 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.37 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.42 (0.24), residues: 1178 helix: -0.13 (0.19), residues: 738 sheet: -2.07 (0.62), residues: 61 loop : -2.24 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 488 TYR 0.019 0.002 TYR A1040 PHE 0.044 0.002 PHE A 934 TRP 0.007 0.001 TRP A 158 HIS 0.010 0.001 HIS A1228 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9339) covalent geometry : angle 0.71673 (12626) hydrogen bonds : bond 0.04920 ( 530) hydrogen bonds : angle 4.94622 ( 1524) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6229 (tmm) cc_final: 0.5522 (tmm) REVERT: A 99 MET cc_start: 0.0537 (mmm) cc_final: 0.0022 (mpp) REVERT: A 107 MET cc_start: 0.5649 (mmm) cc_final: 0.5248 (mtm) REVERT: A 127 ILE cc_start: 0.8834 (mm) cc_final: 0.8619 (mm) REVERT: A 152 MET cc_start: 0.4053 (ptt) cc_final: 0.3208 (ptt) REVERT: A 188 MET cc_start: 0.8256 (mmm) cc_final: 0.8012 (mmp) REVERT: A 271 GLU cc_start: 0.7064 (tp30) cc_final: 0.6324 (pm20) REVERT: A 343 GLN cc_start: 0.7572 (pt0) cc_final: 0.7048 (mm-40) REVERT: A 874 MET cc_start: 0.8496 (tpp) cc_final: 0.8242 (tpp) REVERT: A 885 GLU cc_start: 0.6129 (mt-10) cc_final: 0.5864 (mt-10) REVERT: A 944 MET cc_start: 0.8110 (mmm) cc_final: 0.7109 (mtm) REVERT: A 1014 ILE cc_start: 0.5618 (pt) cc_final: 0.5324 (pt) REVERT: A 1026 MET cc_start: 0.1132 (mpp) cc_final: -0.1113 (ppp) REVERT: A 1162 ASN cc_start: 0.7513 (m-40) cc_final: 0.7027 (p0) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1001 time to fit residues: 23.5830 Evaluate side-chains 128 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 116 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 112 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 ASN ** A1108 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 = 0.4770 r_free = 0.4770 target = 0.181185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.164461 restraints weight = 40126.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.167359 restraints weight = 29573.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.169407 restraints weight = 22573.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.170806 restraints weight = 18209.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.171782 restraints weight = 15405.900| |-----------------------------------------------------------------------------| r_work (final): 0.4686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5011 moved from start: 0.7116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9339 Z= 0.143 Angle : 0.705 10.128 12626 Z= 0.372 Chirality : 0.044 0.203 1456 Planarity : 0.005 0.054 1605 Dihedral : 5.625 32.087 1267 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.54 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.24 (0.24), residues: 1178 helix: -0.04 (0.19), residues: 738 sheet: -1.81 (0.62), residues: 61 loop : -2.08 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 488 TYR 0.031 0.002 TYR A 786 PHE 0.030 0.002 PHE A 196 TRP 0.018 0.001 TRP A 158 HIS 0.007 0.001 HIS A1253 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9339) covalent geometry : angle 0.70453 (12626) hydrogen bonds : bond 0.04770 ( 530) hydrogen bonds : angle 4.82742 ( 1524) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6397 (tmm) cc_final: 0.5733 (tmm) REVERT: A 99 MET cc_start: 0.0667 (mmm) cc_final: 0.0429 (mpp) REVERT: A 127 ILE cc_start: 0.8917 (mm) cc_final: 0.8696 (mm) REVERT: A 152 MET cc_start: 0.4452 (ptt) cc_final: 0.3953 (ptm) REVERT: A 186 ILE cc_start: 0.8242 (pt) cc_final: 0.7560 (pt) REVERT: A 188 MET cc_start: 0.8278 (mmm) cc_final: 0.8056 (mmp) REVERT: A 271 GLU cc_start: 0.7201 (tp30) cc_final: 0.6552 (pm20) REVERT: A 343 GLN cc_start: 0.7562 (pt0) cc_final: 0.6991 (mm-40) REVERT: A 792 MET cc_start: 0.7313 (mtm) cc_final: 0.7099 (mtm) REVERT: A 795 GLN cc_start: 0.6392 (tt0) cc_final: 0.6060 (tp40) REVERT: A 852 GLN cc_start: 0.4470 (pt0) cc_final: 0.3164 (mm-40) REVERT: A 930 LYS cc_start: 0.8958 (tttt) cc_final: 0.8647 (tttt) REVERT: A 944 MET cc_start: 0.8371 (mmm) cc_final: 0.7396 (mtp) REVERT: A 1014 ILE cc_start: 0.6144 (pt) cc_final: 0.5830 (pt) REVERT: A 1026 MET cc_start: 0.0950 (mpp) cc_final: -0.1206 (ppp) REVERT: A 1162 ASN cc_start: 0.7636 (m-40) cc_final: 0.7140 (p0) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.0905 time to fit residues: 20.9563 Evaluate side-chains 128 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 105 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 HIS ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 HIS ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 ASN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 ASN ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.175025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.159382 restraints weight = 40518.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.162525 restraints weight = 28947.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.164572 restraints weight = 21251.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.165929 restraints weight = 16774.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.166873 restraints weight = 13969.624| |-----------------------------------------------------------------------------| r_work (final): 0.4642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5201 moved from start: 0.7820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9339 Z= 0.177 Angle : 0.765 10.303 12626 Z= 0.409 Chirality : 0.046 0.220 1456 Planarity : 0.005 0.053 1605 Dihedral : 5.765 33.046 1267 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.39 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.43 (0.23), residues: 1178 helix: -0.15 (0.18), residues: 739 sheet: -2.21 (0.61), residues: 56 loop : -2.22 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 488 TYR 0.018 0.002 TYR A 243 PHE 0.033 0.003 PHE A1153 TRP 0.010 0.001 TRP A 799 HIS 0.013 0.002 HIS A1253 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9339) covalent geometry : angle 0.76497 (12626) hydrogen bonds : bond 0.04912 ( 530) hydrogen bonds : angle 5.00396 ( 1524) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.4619 (ptt) cc_final: 0.3971 (ptm) REVERT: A 188 MET cc_start: 0.8463 (mmm) cc_final: 0.8218 (mmp) REVERT: A 190 PHE cc_start: 0.8069 (m-10) cc_final: 0.7845 (m-10) REVERT: A 197 PHE cc_start: 0.8915 (t80) cc_final: 0.8671 (t80) REVERT: A 243 TYR cc_start: 0.6737 (t80) cc_final: 0.6080 (t80) REVERT: A 343 GLN cc_start: 0.7780 (pt0) cc_final: 0.7002 (mm110) REVERT: A 775 LYS cc_start: 0.8525 (mptt) cc_final: 0.7682 (pttp) REVERT: A 785 ARG cc_start: 0.5601 (mtt-85) cc_final: 0.4852 (ttm-80) REVERT: A 852 GLN cc_start: 0.4878 (pt0) cc_final: 0.3664 (mm-40) REVERT: A 904 VAL cc_start: 0.7227 (t) cc_final: 0.7011 (t) REVERT: A 930 LYS cc_start: 0.9117 (tttt) cc_final: 0.8892 (ttmt) REVERT: A 944 MET cc_start: 0.8390 (mmm) cc_final: 0.7409 (mtm) REVERT: A 1014 ILE cc_start: 0.6439 (pt) cc_final: 0.6002 (pt) REVERT: A 1162 ASN cc_start: 0.7698 (m-40) cc_final: 0.7072 (p0) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.0934 time to fit residues: 21.3036 Evaluate side-chains 117 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 102 optimal weight: 0.2980 chunk 107 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 58 optimal weight: 0.0570 chunk 22 optimal weight: 6.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 GLN ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 ASN ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.178645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.162298 restraints weight = 39849.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.165534 restraints weight = 28528.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.167762 restraints weight = 20874.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.169275 restraints weight = 16224.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.170345 restraints weight = 13218.988| |-----------------------------------------------------------------------------| r_work (final): 0.4680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5077 moved from start: 0.7955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9339 Z= 0.142 Angle : 0.715 10.478 12626 Z= 0.377 Chirality : 0.045 0.206 1456 Planarity : 0.005 0.064 1605 Dihedral : 5.471 32.563 1267 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.54 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.22 (0.24), residues: 1178 helix: 0.05 (0.19), residues: 732 sheet: -1.86 (0.61), residues: 61 loop : -2.22 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 488 TYR 0.049 0.002 TYR A 110 PHE 0.034 0.002 PHE A 979 TRP 0.012 0.001 TRP A 158 HIS 0.006 0.001 HIS A1253 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9339) covalent geometry : angle 0.71480 (12626) hydrogen bonds : bond 0.04475 ( 530) hydrogen bonds : angle 4.81210 ( 1524) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6363 (tmm) cc_final: 0.5613 (tmm) REVERT: A 74 MET cc_start: 0.7242 (ptt) cc_final: 0.6300 (ptp) REVERT: A 152 MET cc_start: 0.4677 (ptt) cc_final: 0.4100 (ptm) REVERT: A 186 ILE cc_start: 0.8302 (pt) cc_final: 0.7554 (pt) REVERT: A 188 MET cc_start: 0.8373 (mmm) cc_final: 0.8161 (mmp) REVERT: A 197 PHE cc_start: 0.8864 (t80) cc_final: 0.8582 (t80) REVERT: A 243 TYR cc_start: 0.6528 (t80) cc_final: 0.5788 (t80) REVERT: A 343 GLN cc_start: 0.7568 (pt0) cc_final: 0.6956 (mm-40) REVERT: A 775 LYS cc_start: 0.8491 (mptt) cc_final: 0.7678 (pttp) REVERT: A 785 ARG cc_start: 0.5491 (mtt-85) cc_final: 0.4923 (ttm-80) REVERT: A 852 GLN cc_start: 0.4979 (pt0) cc_final: 0.3888 (mm-40) REVERT: A 904 VAL cc_start: 0.7242 (t) cc_final: 0.6997 (t) REVERT: A 928 MET cc_start: 0.7734 (mmp) cc_final: 0.6959 (ttt) REVERT: A 930 LYS cc_start: 0.9217 (tttt) cc_final: 0.8909 (tttt) REVERT: A 944 MET cc_start: 0.8348 (mmm) cc_final: 0.7509 (mtm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1012 time to fit residues: 22.7449 Evaluate side-chains 122 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 91 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 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 = 0.4731 r_free = 0.4731 target = 0.176732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.163701 restraints weight = 43148.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.166441 restraints weight = 30048.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.168502 restraints weight = 21926.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.169896 restraints weight = 16653.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.170904 restraints weight = 13182.363| |-----------------------------------------------------------------------------| r_work (final): 0.4657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5184 moved from start: 0.8475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9339 Z= 0.165 Angle : 0.749 10.104 12626 Z= 0.397 Chirality : 0.046 0.249 1456 Planarity : 0.005 0.081 1605 Dihedral : 5.593 33.158 1267 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.39 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.40 (0.24), residues: 1178 helix: -0.08 (0.18), residues: 742 sheet: -2.09 (0.58), residues: 61 loop : -2.32 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 47 TYR 0.022 0.002 TYR A 359 PHE 0.027 0.002 PHE A 196 TRP 0.013 0.002 TRP A 799 HIS 0.010 0.002 HIS A1253 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9339) covalent geometry : angle 0.74856 (12626) hydrogen bonds : bond 0.04670 ( 530) hydrogen bonds : angle 4.96649 ( 1524) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6004 (tmm) cc_final: 0.5258 (tmm) REVERT: A 110 TYR cc_start: 0.3954 (m-10) cc_final: 0.3614 (m-80) REVERT: A 138 ARG cc_start: 0.6806 (ptt180) cc_final: 0.6458 (ptt180) REVERT: A 152 MET cc_start: 0.4723 (ptt) cc_final: 0.4144 (ptm) REVERT: A 188 MET cc_start: 0.8433 (mmm) cc_final: 0.8177 (mmp) REVERT: A 197 PHE cc_start: 0.8751 (t80) cc_final: 0.8413 (t80) REVERT: A 237 ASP cc_start: 0.7156 (t0) cc_final: 0.6252 (p0) REVERT: A 243 TYR cc_start: 0.6667 (t80) cc_final: 0.6056 (t80) REVERT: A 343 GLN cc_start: 0.7511 (pt0) cc_final: 0.6884 (mm-40) REVERT: A 775 LYS cc_start: 0.8419 (mptt) cc_final: 0.7668 (pttp) REVERT: A 785 ARG cc_start: 0.5615 (mtt-85) cc_final: 0.5054 (ttm-80) REVERT: A 904 VAL cc_start: 0.7136 (t) cc_final: 0.6885 (t) REVERT: A 928 MET cc_start: 0.7687 (mmp) cc_final: 0.6940 (ttt) REVERT: A 944 MET cc_start: 0.8165 (mmm) cc_final: 0.7415 (mtm) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1015 time to fit residues: 22.5394 Evaluate side-chains 120 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 64 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 110 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1178 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 = 0.4757 r_free = 0.4757 target = 0.179118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.166147 restraints weight = 42976.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.169018 restraints weight = 30004.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.171000 restraints weight = 21725.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.172405 restraints weight = 16473.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.173453 restraints weight = 12973.393| |-----------------------------------------------------------------------------| r_work (final): 0.4706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5056 moved from start: 0.8713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9339 Z= 0.140 Angle : 0.732 9.910 12626 Z= 0.382 Chirality : 0.045 0.204 1456 Planarity : 0.005 0.049 1605 Dihedral : 5.409 30.861 1267 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.45 % Favored : 93.21 % Rotamer: Outliers : 0.10 % Allowed : 0.72 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.22 (0.24), residues: 1178 helix: 0.00 (0.19), residues: 737 sheet: -2.08 (0.63), residues: 56 loop : -2.09 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 258 TYR 0.016 0.002 TYR A 946 PHE 0.029 0.002 PHE A 190 TRP 0.011 0.001 TRP A 799 HIS 0.006 0.001 HIS A1253 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9339) covalent geometry : angle 0.73216 (12626) hydrogen bonds : bond 0.04392 ( 530) hydrogen bonds : angle 4.84265 ( 1524) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.5926 (tmm) cc_final: 0.5250 (tmm) REVERT: A 126 TYR cc_start: 0.6827 (t80) cc_final: 0.6410 (t80) REVERT: A 152 MET cc_start: 0.4637 (ptt) cc_final: 0.4046 (ptm) REVERT: A 186 ILE cc_start: 0.8227 (pt) cc_final: 0.7705 (pt) REVERT: A 188 MET cc_start: 0.8287 (mmm) cc_final: 0.8013 (mmp) REVERT: A 193 MET cc_start: 0.9180 (mmm) cc_final: 0.8666 (mmp) REVERT: A 197 PHE cc_start: 0.8647 (t80) cc_final: 0.8279 (t80) REVERT: A 237 ASP cc_start: 0.7076 (t0) cc_final: 0.6225 (p0) REVERT: A 343 GLN cc_start: 0.7169 (pt0) cc_final: 0.6728 (mm-40) REVERT: A 775 LYS cc_start: 0.8325 (mptt) cc_final: 0.7687 (pttp) REVERT: A 904 VAL cc_start: 0.6949 (t) cc_final: 0.6701 (t) REVERT: A 928 MET cc_start: 0.7800 (mmp) cc_final: 0.6968 (ttt) REVERT: A 944 MET cc_start: 0.8013 (mmm) cc_final: 0.7511 (mtm) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.0988 time to fit residues: 21.5168 Evaluate side-chains 124 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 101 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 46 optimal weight: 0.4980 chunk 62 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 29 optimal weight: 0.0060 chunk 107 optimal weight: 1.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 918 GLN ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.179467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.166870 restraints weight = 42886.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.169664 restraints weight = 29742.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.171632 restraints weight = 21610.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.173021 restraints weight = 16331.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.174058 restraints weight = 12801.376| |-----------------------------------------------------------------------------| r_work (final): 0.4691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5102 moved from start: 0.8988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9339 Z= 0.141 Angle : 0.732 9.809 12626 Z= 0.383 Chirality : 0.045 0.203 1456 Planarity : 0.005 0.052 1605 Dihedral : 5.359 30.333 1267 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.96 % Favored : 92.61 % Rotamer: Outliers : 0.10 % Allowed : 0.20 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.28 (0.24), residues: 1178 helix: -0.06 (0.18), residues: 743 sheet: -1.81 (0.60), residues: 61 loop : -2.17 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 785 TYR 0.024 0.002 TYR A 243 PHE 0.028 0.002 PHE A 190 TRP 0.008 0.001 TRP A 799 HIS 0.006 0.001 HIS A1253 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9339) covalent geometry : angle 0.73157 (12626) hydrogen bonds : bond 0.04410 ( 530) hydrogen bonds : angle 4.84184 ( 1524) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6054 (tmm) cc_final: 0.5304 (tmm) REVERT: A 110 TYR cc_start: 0.3434 (m-10) cc_final: 0.3148 (m-10) REVERT: A 126 TYR cc_start: 0.6868 (t80) cc_final: 0.6442 (t80) REVERT: A 152 MET cc_start: 0.4679 (ptt) cc_final: 0.4081 (ptm) REVERT: A 186 ILE cc_start: 0.8315 (pt) cc_final: 0.7801 (pt) REVERT: A 188 MET cc_start: 0.8227 (mmm) cc_final: 0.8011 (mmp) REVERT: A 193 MET cc_start: 0.9217 (mmm) cc_final: 0.8704 (mmp) REVERT: A 197 PHE cc_start: 0.8664 (t80) cc_final: 0.8300 (t80) REVERT: A 237 ASP cc_start: 0.7171 (t0) cc_final: 0.6293 (p0) REVERT: A 343 GLN cc_start: 0.7077 (pt0) cc_final: 0.6558 (mm-40) REVERT: A 775 LYS cc_start: 0.8375 (mptt) cc_final: 0.7693 (pttp) REVERT: A 904 VAL cc_start: 0.7011 (t) cc_final: 0.6738 (t) REVERT: A 928 MET cc_start: 0.7927 (mmp) cc_final: 0.7089 (ttt) REVERT: A 944 MET cc_start: 0.7985 (mmm) cc_final: 0.7494 (mtm) REVERT: A 1014 ILE cc_start: 0.6707 (pt) cc_final: 0.6390 (pt) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.0990 time to fit residues: 21.9646 Evaluate side-chains 124 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 3 optimal weight: 0.0040 chunk 68 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 0.0470 chunk 106 optimal weight: 0.4980 chunk 23 optimal weight: 0.0570 overall best weight: 0.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 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 = 0.4781 r_free = 0.4781 target = 0.181469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.168525 restraints weight = 42780.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.171227 restraints weight = 30045.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.173201 restraints weight = 22013.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.174639 restraints weight = 16758.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.175719 restraints weight = 13196.025| |-----------------------------------------------------------------------------| r_work (final): 0.4733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4985 moved from start: 0.9132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9339 Z= 0.136 Angle : 0.710 9.868 12626 Z= 0.370 Chirality : 0.044 0.199 1456 Planarity : 0.004 0.052 1605 Dihedral : 5.175 28.837 1267 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.77 % Favored : 93.89 % Rotamer: Outliers : 0.10 % Allowed : 0.72 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.14 (0.24), residues: 1178 helix: 0.09 (0.19), residues: 733 sheet: -1.57 (0.63), residues: 61 loop : -2.17 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 785 TYR 0.019 0.001 TYR A 946 PHE 0.030 0.002 PHE A 190 TRP 0.008 0.001 TRP A 208 HIS 0.004 0.001 HIS A1253 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9339) covalent geometry : angle 0.70982 (12626) hydrogen bonds : bond 0.04250 ( 530) hydrogen bonds : angle 4.73250 ( 1524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1640.09 seconds wall clock time: 29 minutes 0.73 seconds (1740.73 seconds total)