Starting phenix.real_space_refine on Sat Sep 12 07:17:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qex_4539/09_2026/6qex_4539.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qex_4539/09_2026/6qex_4539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qex_4539/09_2026/6qex_4539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qex_4539/09_2026/6qex_4539.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6qex_4539/09_2026/6qex_4539.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qex_4539/09_2026/6qex_4539.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qex_4539/09_2026/6qex_4539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qex_4539/09_2026/6qex_4539.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 526 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 53 5.16 5 C 8648 2.51 5 N 2131 2.21 5 O 2417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.11s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13251 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1182, 9191 Classifications: {'peptide': 1182} Link IDs: {'PTRANS': 27, 'TRANS': 1154} Chain breaks: 1 Chain: "B" Number of atoms: 1713 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} bond proxies already assigned to first conformer: 1747 Chain: "C" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1717 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 211} Chain: "A" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 630 Unusual residues: {'3PE': 2, 'CLR': 16, 'NAG': 3, 'TA1': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.80, per 1000 atoms: 0.21 Number of scatterers: 13251 At special positions: 0 Unit cell: (89.04, 101.64, 210, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 P 2 15.00 O 2417 8.00 N 2131 7.00 C 8648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.04 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG ACYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG BCYS B 200 " distance=2.05 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS C 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS C 204 " distance=2.03 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=1, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 91 " " NAG A1302 " - " ASN A 94 " " NAG A1303 " - " ASN A 99 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 563.6 milliseconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3004 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 13 sheets defined 51.8% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 35 through 40 removed outlier: 4.107A pdb=" N PHE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 63 removed outlier: 3.698A pdb=" N VAL A 52 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 93 removed outlier: 3.756A pdb=" N VAL A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 156 removed outlier: 3.972A pdb=" N LEU A 107 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 168 through 186 removed outlier: 3.681A pdb=" N ASN A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 211 removed outlier: 3.528A pdb=" N PHE A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.674A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Proline residue: A 223 - end of helix removed outlier: 3.520A pdb=" N SER A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 removed outlier: 3.684A pdb=" N LEU A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 260 removed outlier: 3.614A pdb=" N ALA A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 269 through 323 removed outlier: 3.672A pdb=" N GLU A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 348 removed outlier: 3.562A pdb=" N VAL A 331 " --> pdb=" O SER A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 371 removed outlier: 4.128A pdb=" N ILE A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 441 removed outlier: 3.686A pdb=" N GLN A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.875A pdb=" N THR A 460 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.836A pdb=" N ILE A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 490 Processing helix chain 'A' and resid 496 through 508 Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 525 through 529 removed outlier: 3.736A pdb=" N GLY A 528 " --> pdb=" O GLY A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 546 Processing helix chain 'A' and resid 562 through 576 removed outlier: 3.525A pdb=" N GLU A 566 " --> pdb=" O ASP A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 619 removed outlier: 3.534A pdb=" N LYS A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 700 through 705 removed outlier: 3.721A pdb=" N LEU A 705 " --> pdb=" O LYS A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 723 removed outlier: 3.946A pdb=" N PHE A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 723 " --> pdb=" O ILE A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 739 Processing helix chain 'A' and resid 744 through 798 removed outlier: 4.304A pdb=" N LEU A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 805 removed outlier: 3.606A pdb=" N PHE A 804 " --> pdb=" O ASP A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 820 Processing helix chain 'A' and resid 829 through 854 removed outlier: 4.913A pdb=" N THR A 845 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY A 846 " --> pdb=" O ASN A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 880 Proline residue: A 866 - end of helix removed outlier: 3.785A pdb=" N GLU A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 880 " --> pdb=" O MET A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 894 removed outlier: 3.918A pdb=" N LYS A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 903 removed outlier: 3.998A pdb=" N THR A 898 " --> pdb=" O GLY A 894 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 903 " --> pdb=" O GLU A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 911 removed outlier: 3.694A pdb=" N VAL A 907 " --> pdb=" O ASN A 903 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 924 removed outlier: 3.826A pdb=" N PHE A 916 " --> pdb=" O GLN A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 966 removed outlier: 3.563A pdb=" N ARG A 929 " --> pdb=" O GLN A 925 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY A 939 " --> pdb=" O ALA A 935 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TYR A 950 " --> pdb=" O GLN A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 993 Processing helix chain 'A' and resid 998 through 1014 removed outlier: 3.508A pdb=" N LYS A1014 " --> pdb=" O MET A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1084 Processing helix chain 'A' and resid 1105 through 1113 removed outlier: 3.883A pdb=" N LEU A1109 " --> pdb=" O ASN A1105 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A1113 " --> pdb=" O LEU A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1133 Processing helix chain 'A' and resid 1141 through 1152 Processing helix chain 'A' and resid 1154 through 1161 removed outlier: 3.770A pdb=" N LEU A1161 " --> pdb=" O PHE A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1174 removed outlier: 3.896A pdb=" N GLY A1173 " --> pdb=" O GLY A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1191 Processing helix chain 'A' and resid 1207 through 1222 removed outlier: 3.945A pdb=" N LYS A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A1218 " --> pdb=" O VAL A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1239 removed outlier: 4.235A pdb=" N ASN A1239 " --> pdb=" O SER A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1263 Processing helix chain 'A' and resid 1265 through 1272 removed outlier: 3.632A pdb=" N SER A1269 " --> pdb=" O GLY A1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 133 Processing helix chain 'B' and resid 191 through 195 removed outlier: 3.704A pdb=" N ARG B 194 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS B 195 " --> pdb=" O TYR B 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 191 through 195' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing sheet with id=AA1, first strand: chain 'A' and resid 415 through 417 removed outlier: 3.744A pdb=" N ARG A 395 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 450 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL A 397 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLU A 448 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 470 through 473 removed outlier: 6.551A pdb=" N GLY A 471 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ASP A 555 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 473 " --> pdb=" O ASP A 555 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL A 423 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY A 600 " --> pdb=" O VAL A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1056 through 1060 removed outlier: 5.226A pdb=" N LEU A1056 " --> pdb=" O GLU A1039 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL A1040 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ALA A1091 " --> pdb=" O VAL A1040 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1114 through 1116 removed outlier: 4.022A pdb=" N LEU A1198 " --> pdb=" O GLY A1114 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A1116 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP A1200 " --> pdb=" O VAL A1116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A1068 " --> pdb=" O VAL A1229 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA A1067 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N PHE A1246 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A1069 " --> pdb=" O PHE A1246 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A1245 " --> pdb=" O LYS A1252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 23 Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 53 removed outlier: 5.166A pdb=" N LEU B 51 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU B 42 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 124 removed outlier: 3.910A pdb=" N ASN B 143 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR B 179 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 161 removed outlier: 4.520A pdb=" N TRP B 154 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN B 151 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.794A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE C 34 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 99 " --> pdb=" O TYR C 33 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 129 through 133 removed outlier: 4.127A pdb=" N GLY C 148 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS C 149 " --> pdb=" O SER C 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 129 through 133 removed outlier: 4.127A pdb=" N GLY C 148 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS C 149 " --> pdb=" O SER C 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 160 through 163 removed outlier: 3.654A pdb=" N THR C 160 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 207 " --> pdb=" O THR C 160 " (cutoff:3.500A) 715 hydrogen bonds defined for protein. 2030 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: 2.53 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2085 1.30 - 1.44: 3518 1.44 - 1.57: 7870 1.57 - 1.70: 5 1.70 - 1.83: 87 Bond restraints: 13565 Sorted by residual: bond pdb=" C7 NAG A1302 " pdb=" N2 NAG A1302 " ideal model delta sigma weight residual 1.346 1.492 -0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" C7 NAG A1303 " pdb=" N2 NAG A1303 " ideal model delta sigma weight residual 1.346 1.492 -0.146 2.00e-02 2.50e+03 5.31e+01 bond pdb=" C7 NAG A1301 " pdb=" N2 NAG A1301 " ideal model delta sigma weight residual 1.346 1.482 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C10 TA1 A1320 " pdb=" C18 TA1 A1320 " ideal model delta sigma weight residual 1.611 1.490 0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.521 -0.115 2.00e-02 2.50e+03 3.33e+01 ... (remaining 13560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.71: 18265 4.71 - 9.42: 179 9.42 - 14.13: 15 14.13 - 18.84: 2 18.84 - 23.55: 2 Bond angle restraints: 18463 Sorted by residual: angle pdb=" N SER A 90 " pdb=" CA SER A 90 " pdb=" C SER A 90 " ideal model delta sigma weight residual 111.28 121.42 -10.14 1.09e+00 8.42e-01 8.65e+01 angle pdb=" N GLU A 86 " pdb=" CA GLU A 86 " pdb=" C GLU A 86 " ideal model delta sigma weight residual 111.28 120.68 -9.40 1.09e+00 8.42e-01 7.43e+01 angle pdb=" O12 3PE A1322 " pdb=" P 3PE A1322 " pdb=" O14 3PE A1322 " ideal model delta sigma weight residual 123.79 100.24 23.55 3.00e+00 1.11e-01 6.16e+01 angle pdb=" O12 3PE A1321 " pdb=" P 3PE A1321 " pdb=" O14 3PE A1321 " ideal model delta sigma weight residual 123.79 100.99 22.80 3.00e+00 1.11e-01 5.77e+01 angle pdb=" C SER B 94 " pdb=" N GLN B 95 " pdb=" CA GLN B 95 " ideal model delta sigma weight residual 121.70 133.42 -11.72 1.80e+00 3.09e-01 4.24e+01 ... (remaining 18458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6925 17.98 - 35.97: 761 35.97 - 53.95: 140 53.95 - 71.93: 39 71.93 - 89.92: 9 Dihedral angle restraints: 7874 sinusoidal: 3189 harmonic: 4685 Sorted by residual: dihedral pdb=" CB CYS B 220 " pdb=" SG CYS B 220 " pdb=" SG CYS C 137 " pdb=" CB CYS C 137 " ideal model delta sinusoidal sigma weight residual -86.00 -173.43 87.43 1 1.00e+01 1.00e-02 9.17e+01 dihedral pdb=" CA LYS B 55 " pdb=" C LYS B 55 " pdb=" N VAL B 56 " pdb=" CA VAL B 56 " ideal model delta harmonic sigma weight residual -180.00 -136.40 -43.60 0 5.00e+00 4.00e-02 7.61e+01 dihedral pdb=" CA PRO B 100 " pdb=" C PRO B 100 " pdb=" N PRO B 101 " pdb=" CA PRO B 101 " ideal model delta harmonic sigma weight residual 180.00 150.18 29.82 0 5.00e+00 4.00e-02 3.56e+01 ... (remaining 7871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 2121 0.329 - 0.657: 26 0.657 - 0.986: 1 0.986 - 1.315: 2 1.315 - 1.644: 2 Chirality restraints: 2152 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 91 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-01 2.50e+01 6.75e+01 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 94 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -0.92 -1.48 2.00e-01 2.50e+01 5.45e+01 chirality pdb=" C10 TA1 A1320 " pdb=" C02 TA1 A1320 " pdb=" C11 TA1 A1320 " pdb=" C18 TA1 A1320 " both_signs ideal model delta sigma weight residual False 2.54 1.25 1.29 2.00e-01 2.50e+01 4.16e+01 ... (remaining 2149 not shown) Planarity restraints: 2229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C29 TA1 A1320 " 0.264 2.00e-02 2.50e+03 2.29e-01 6.57e+02 pdb=" C30 TA1 A1320 " -0.058 2.00e-02 2.50e+03 pdb=" C31 TA1 A1320 " -0.021 2.00e-02 2.50e+03 pdb=" N01 TA1 A1320 " -0.386 2.00e-02 2.50e+03 pdb=" O14 TA1 A1320 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 94 " 0.017 2.00e-02 2.50e+03 1.04e-01 1.36e+02 pdb=" CG ASN A 94 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 94 " 0.077 2.00e-02 2.50e+03 pdb=" ND2 ASN A 94 " -0.184 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 99 " -0.037 2.00e-02 2.50e+03 6.22e-02 4.84e+01 pdb=" CG ASN A 99 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 99 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 99 " 0.110 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " -0.074 2.00e-02 2.50e+03 ... (remaining 2226 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.10: 3 2.10 - 2.80: 3546 2.80 - 3.50: 17424 3.50 - 4.20: 29017 4.20 - 4.90: 51313 Nonbonded interactions: 101303 Sorted by model distance: nonbonded pdb=" CD1 ILE A 92 " pdb=" CD PRO B 100 " model vdw 1.406 3.860 nonbonded pdb=" ND2 ASN A 84 " pdb=" O THR A 740 " model vdw 1.623 3.120 nonbonded pdb=" CD1 ILE A 92 " pdb=" CG PRO B 100 " model vdw 1.999 3.860 nonbonded pdb=" O ILE A 700 " pdb=" CD1 ILE A 829 " model vdw 2.217 3.460 nonbonded pdb=" OG1 THR A1203 " pdb=" OE1 GLU A1211 " model vdw 2.256 3.040 ... (remaining 101298 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 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: 4.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.310 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 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 : 0.010 0.468 13575 Z= 0.602 Angle : 1.358 41.778 18484 Z= 0.632 Chirality : 0.103 1.644 2152 Planarity : 0.008 0.229 2226 Dihedral : 15.513 89.919 4852 Min Nonbonded Distance : 1.406 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.99 % Favored : 93.95 % Rotamer: Outliers : 0.73 % Allowed : 8.53 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.39 (0.17), residues: 1620 helix: -1.96 (0.14), residues: 774 sheet: -1.77 (0.28), residues: 300 loop : -2.64 (0.22), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 98 TYR 0.029 0.003 TYR A 920 PHE 0.033 0.003 PHE C 50 TRP 0.075 0.003 TRP B 102 HIS 0.006 0.002 HIS B 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00937 / 0.43 (13565) covalent geometry : angle 1.23560 / 0.60 (18463) SS BOND : bond 0.00980 / 0.52 ( 6) SS BOND : angle 2.06412 / 1.05 ( 12) hydrogen bonds : bond 0.13940 / 9.39 ( 703) hydrogen bonds : angle 6.34489 / 4.67 ( 2030) Misc. bond : bond 0.46850 / 31.23 ( 1) link_NAG-ASN : bond 0.14114 / 7.00 ( 3) link_NAG-ASN : angle 25.47653 / 15.53 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.4564 (OUTLIER) cc_final: 0.2434 (mtt90) REVERT: A 155 ILE cc_start: 0.7632 (tt) cc_final: 0.7398 (tt) REVERT: A 757 LEU cc_start: 0.8594 (tp) cc_final: 0.8372 (mt) REVERT: A 862 LEU cc_start: 0.9164 (mt) cc_final: 0.8964 (mm) REVERT: B 4 MET cc_start: 0.8779 (mmm) cc_final: 0.8480 (mmm) REVERT: B 99 ILE cc_start: 0.8898 (pt) cc_final: 0.8634 (pt) REVERT: C 110 ASP cc_start: 0.8743 (p0) cc_final: 0.8516 (p0) REVERT: C 131 TYR cc_start: 0.8500 (m-80) cc_final: 0.8209 (m-80) REVERT: C 180 GLN cc_start: 0.7688 (pp30) cc_final: 0.7298 (pp30) outliers start: 10 outliers final: 3 residues processed: 184 average time/residue: 0.1236 time to fit residues: 33.2347 Evaluate side-chains 122 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 1242 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 ASN A 438 GLN A 508 ASN ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 GLN A 750 GLN A 773 GLN A 838 GLN A 839 ASN A1054 GLN A1105 ASN ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 HIS A1239 ASN A1248 ASN B 130 GLN B 144 ASN B 216 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.209020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.178274 restraints weight = 20034.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.178024 restraints weight = 40989.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.174396 restraints weight = 18811.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.174277 restraints weight = 21475.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.174509 restraints weight = 12052.664| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13575 Z= 0.152 Angle : 0.678 9.301 18484 Z= 0.340 Chirality : 0.043 0.247 2152 Planarity : 0.005 0.054 2226 Dihedral : 8.679 65.697 1957 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.26 % Favored : 95.68 % Rotamer: Outliers : 2.41 % Allowed : 12.39 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.66 (0.19), residues: 1620 helix: -0.13 (0.18), residues: 790 sheet: -1.28 (0.29), residues: 297 loop : -2.34 (0.23), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 798 TYR 0.018 0.002 TYR A 953 PHE 0.020 0.001 PHE B 92 TRP 0.020 0.001 TRP B 102 HIS 0.007 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (13565) covalent geometry : angle 0.66767 / 0.34 (18463) SS BOND : bond 0.01065 / 0.71 ( 6) SS BOND : angle 0.99648 / 0.56 ( 12) hydrogen bonds : bond 0.05390 / 3.57 ( 703) hydrogen bonds : angle 4.72988 / 3.49 ( 2030) Misc. bond : bond 0.00016 / 0.01 ( 1) link_NAG-ASN : bond 0.01459 / 1.03 ( 3) link_NAG-ASN : angle 5.18881 / 2.98 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 MET cc_start: 0.4238 (mmm) cc_final: 0.3878 (mpp) REVERT: A 850 SER cc_start: 0.8223 (t) cc_final: 0.8010 (t) REVERT: A 953 TYR cc_start: 0.7595 (OUTLIER) cc_final: 0.6783 (t80) REVERT: A 1193 GLN cc_start: 0.5999 (pp30) cc_final: 0.5145 (pm20) REVERT: B 4 MET cc_start: 0.8389 (mmm) cc_final: 0.8178 (mmm) REVERT: B 99 ILE cc_start: 0.8645 (pt) cc_final: 0.8434 (pt) REVERT: C 182 ASP cc_start: 0.7688 (p0) cc_final: 0.7462 (p0) REVERT: C 183 LEU cc_start: 0.8523 (mp) cc_final: 0.8273 (mp) outliers start: 33 outliers final: 10 residues processed: 162 average time/residue: 0.1146 time to fit residues: 27.9150 Evaluate side-chains 122 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 202 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 139 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 116 optimal weight: 30.0000 chunk 94 optimal weight: 20.0000 chunk 153 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 508 ASN ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 HIS ** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS C 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.207756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.178667 restraints weight = 21569.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.176768 restraints weight = 40146.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.173641 restraints weight = 20633.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.173807 restraints weight = 23051.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.174249 restraints weight = 12327.340| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4123 r_free = 0.4123 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4123 r_free = 0.4123 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13575 Z= 0.162 Angle : 0.662 9.145 18484 Z= 0.332 Chirality : 0.043 0.229 2152 Planarity : 0.004 0.060 2226 Dihedral : 8.243 64.964 1950 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.43 % Allowed : 15.45 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.20), residues: 1620 helix: 0.51 (0.18), residues: 792 sheet: -0.99 (0.30), residues: 298 loop : -2.13 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 161 TYR 0.019 0.002 TYR C 131 PHE 0.022 0.001 PHE B 92 TRP 0.021 0.001 TRP B 102 HIS 0.004 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (13565) covalent geometry : angle 0.64803 / 0.33 (18463) SS BOND : bond 0.00580 / 0.30 ( 6) SS BOND : angle 3.04703 / 2.20 ( 12) hydrogen bonds : bond 0.05234 / 3.47 ( 703) hydrogen bonds : angle 4.59214 / 3.40 ( 2030) Misc. bond : bond 0.00024 / 0.02 ( 1) link_NAG-ASN : bond 0.00848 / 0.59 ( 3) link_NAG-ASN : angle 5.03275 / 2.65 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 110 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.7635 (ttp) cc_final: 0.7307 (ttp) REVERT: A 95 ARG cc_start: 0.5548 (OUTLIER) cc_final: 0.5145 (ptm160) REVERT: A 468 GLU cc_start: 0.5819 (tp30) cc_final: 0.5396 (pt0) REVERT: A 850 SER cc_start: 0.8299 (t) cc_final: 0.8088 (t) REVERT: A 948 MET cc_start: 0.7662 (tpp) cc_final: 0.7376 (tpp) REVERT: A 953 TYR cc_start: 0.7556 (OUTLIER) cc_final: 0.6712 (t80) REVERT: B 4 MET cc_start: 0.8441 (mmm) cc_final: 0.8220 (mmm) REVERT: B 99 ILE cc_start: 0.8656 (pt) cc_final: 0.8436 (pt) outliers start: 45 outliers final: 28 residues processed: 145 average time/residue: 0.1171 time to fit residues: 25.6848 Evaluate side-chains 130 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 202 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 47 optimal weight: 0.2980 chunk 57 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 138 optimal weight: 0.0170 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.212210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.183791 restraints weight = 25561.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.182307 restraints weight = 44811.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.179022 restraints weight = 20767.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.179080 restraints weight = 21817.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.179370 restraints weight = 11955.145| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4166 r_free = 0.4166 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4166 r_free = 0.4166 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13575 Z= 0.116 Angle : 0.596 8.827 18484 Z= 0.299 Chirality : 0.041 0.203 2152 Planarity : 0.004 0.063 2226 Dihedral : 7.789 66.286 1950 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.83 % Favored : 96.11 % Rotamer: Outliers : 2.48 % Allowed : 17.57 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.21), residues: 1620 helix: 1.06 (0.19), residues: 792 sheet: -0.67 (0.30), residues: 298 loop : -1.89 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 161 TYR 0.024 0.001 TYR C 131 PHE 0.021 0.001 PHE A 399 TRP 0.013 0.001 TRP A 698 HIS 0.002 0.000 HIS B 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (13565) covalent geometry : angle 0.58431 / 0.30 (18463) SS BOND : bond 0.00385 / 0.21 ( 6) SS BOND : angle 1.60644 / 1.01 ( 12) hydrogen bonds : bond 0.04398 / 2.90 ( 703) hydrogen bonds : angle 4.23362 / 3.11 ( 2030) Misc. bond : bond 0.00029 / 0.02 ( 1) link_NAG-ASN : bond 0.00430 / 0.27 ( 3) link_NAG-ASN : angle 5.08585 / 2.75 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7416 (ttp) cc_final: 0.7114 (ttp) REVERT: A 95 ARG cc_start: 0.5468 (OUTLIER) cc_final: 0.5147 (ptm160) REVERT: A 314 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7934 (m-10) REVERT: A 497 MET cc_start: 0.4171 (mmm) cc_final: 0.3854 (mpp) REVERT: A 724 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7856 (mp) REVERT: A 850 SER cc_start: 0.8247 (t) cc_final: 0.8023 (t) REVERT: A 948 MET cc_start: 0.7605 (tpp) cc_final: 0.7271 (tpp) REVERT: A 953 TYR cc_start: 0.7239 (OUTLIER) cc_final: 0.6679 (t80) REVERT: A 1010 MET cc_start: 0.7031 (tmm) cc_final: 0.6750 (tmm) outliers start: 32 outliers final: 19 residues processed: 138 average time/residue: 0.0995 time to fit residues: 21.5409 Evaluate side-chains 129 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 202 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 112 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 63 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 87 optimal weight: 0.2980 chunk 96 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 518 HIS ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1130 ASN ** A1153 ASN ** 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 = 0.4513 r_free = 0.4513 target = 0.210789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.180088 restraints weight = 18159.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.181261 restraints weight = 42222.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.180758 restraints weight = 20326.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.180788 restraints weight = 15329.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.181231 restraints weight = 12429.593| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4203 r_free = 0.4203 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4203 r_free = 0.4203 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13575 Z= 0.128 Angle : 0.601 8.697 18484 Z= 0.301 Chirality : 0.041 0.191 2152 Planarity : 0.004 0.055 2226 Dihedral : 7.696 66.521 1950 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.92 % Allowed : 18.59 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1620 helix: 1.22 (0.19), residues: 791 sheet: -0.56 (0.31), residues: 298 loop : -1.80 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 217 TYR 0.014 0.001 TYR A 953 PHE 0.019 0.001 PHE B 92 TRP 0.012 0.001 TRP A 232 HIS 0.003 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (13565) covalent geometry : angle 0.59316 / 0.30 (18463) SS BOND : bond 0.00541 / 0.30 ( 6) SS BOND : angle 1.26859 / 0.83 ( 12) hydrogen bonds : bond 0.04467 / 2.96 ( 703) hydrogen bonds : angle 4.24857 / 3.13 ( 2030) Misc. bond : bond 0.00026 / 0.02 ( 1) link_NAG-ASN : bond 0.00701 / 0.49 ( 3) link_NAG-ASN : angle 4.24942 / 2.18 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.471 Fit side-chains REVERT: A 75 MET cc_start: 0.7507 (ttp) cc_final: 0.7294 (ttp) REVERT: A 314 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7966 (m-10) REVERT: A 850 SER cc_start: 0.8201 (t) cc_final: 0.7976 (t) REVERT: A 948 MET cc_start: 0.7544 (tpp) cc_final: 0.7221 (tpp) REVERT: A 953 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6723 (t80) REVERT: A 1010 MET cc_start: 0.6790 (tmm) cc_final: 0.6503 (tmm) REVERT: C 182 ASP cc_start: 0.7406 (p0) cc_final: 0.7205 (p0) outliers start: 38 outliers final: 22 residues processed: 140 average time/residue: 0.0989 time to fit residues: 21.5623 Evaluate side-chains 126 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 202 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 157 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 57 optimal weight: 0.0770 chunk 1 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.209316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.181019 restraints weight = 19184.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.179277 restraints weight = 41966.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.175941 restraints weight = 21734.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.174618 restraints weight = 27270.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.175375 restraints weight = 14685.626| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4119 r_free = 0.4119 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4119 r_free = 0.4119 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 13575 Z= 0.145 Angle : 0.619 11.923 18484 Z= 0.310 Chirality : 0.042 0.240 2152 Planarity : 0.006 0.217 2226 Dihedral : 7.408 65.974 1946 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.57 % Allowed : 19.10 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.21), residues: 1620 helix: 1.26 (0.18), residues: 787 sheet: -0.59 (0.31), residues: 303 loop : -1.68 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.001 ARG A 148 TYR 0.014 0.001 TYR A 953 PHE 0.020 0.001 PHE B 92 TRP 0.014 0.001 TRP B 102 HIS 0.003 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (13565) covalent geometry : angle 0.61044 / 0.31 (18463) SS BOND : bond 0.00526 / 0.29 ( 6) SS BOND : angle 1.30858 / 0.86 ( 12) hydrogen bonds : bond 0.04711 / 3.15 ( 703) hydrogen bonds : angle 4.29777 / 3.17 ( 2030) Misc. bond : bond 0.00705 / 0.47 ( 1) link_NAG-ASN : bond 0.00684 / 0.48 ( 3) link_NAG-ASN : angle 4.56297 / 2.16 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 102 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7709 (ttp) cc_final: 0.7451 (ttp) REVERT: A 314 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7988 (m-10) REVERT: A 850 SER cc_start: 0.8223 (t) cc_final: 0.7986 (t) REVERT: A 948 MET cc_start: 0.7594 (tpp) cc_final: 0.7245 (tpp) REVERT: A 953 TYR cc_start: 0.7267 (OUTLIER) cc_final: 0.6644 (t80) REVERT: A 1010 MET cc_start: 0.6939 (tmm) cc_final: 0.6613 (tmm) REVERT: A 1061 LYS cc_start: 0.5982 (tptp) cc_final: 0.5252 (ttpp) REVERT: C 182 ASP cc_start: 0.7471 (p0) cc_final: 0.7153 (p0) outliers start: 47 outliers final: 32 residues processed: 143 average time/residue: 0.0929 time to fit residues: 21.3942 Evaluate side-chains 135 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 926 VAL Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 202 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 77 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 108 optimal weight: 50.0000 chunk 124 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.210017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.184378 restraints weight = 26668.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.182411 restraints weight = 48239.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.178964 restraints weight = 20959.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.179543 restraints weight = 15916.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.179858 restraints weight = 9529.778| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4153 r_free = 0.4153 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4153 r_free = 0.4153 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13575 Z= 0.190 Angle : 0.677 10.121 18484 Z= 0.339 Chirality : 0.044 0.254 2152 Planarity : 0.005 0.169 2226 Dihedral : 7.678 63.637 1946 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.25 % Favored : 94.69 % Rotamer: Outliers : 3.94 % Allowed : 20.04 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.21), residues: 1620 helix: 1.11 (0.18), residues: 786 sheet: -0.52 (0.31), residues: 296 loop : -1.80 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG A 148 TYR 0.016 0.002 TYR A 130 PHE 0.024 0.002 PHE B 92 TRP 0.019 0.001 TRP B 102 HIS 0.004 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (13565) covalent geometry : angle 0.67068 / 0.34 (18463) SS BOND : bond 0.00689 / 0.41 ( 6) SS BOND : angle 1.54117 / 1.02 ( 12) hydrogen bonds : bond 0.05275 / 3.51 ( 703) hydrogen bonds : angle 4.54615 / 3.35 ( 2030) Misc. bond : bond 0.00522 / 0.35 ( 1) link_NAG-ASN : bond 0.00848 / 0.59 ( 3) link_NAG-ASN : angle 4.04708 / 1.96 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 104 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7835 (ttp) cc_final: 0.7476 (ttp) REVERT: A 314 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.8089 (m-10) REVERT: A 443 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5766 (mp) REVERT: A 497 MET cc_start: 0.3986 (mmm) cc_final: 0.3557 (mpp) REVERT: A 850 SER cc_start: 0.8368 (t) cc_final: 0.8132 (t) REVERT: A 953 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.6602 (t80) REVERT: B 5 THR cc_start: 0.8741 (m) cc_final: 0.8446 (p) REVERT: C 182 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7167 (p0) outliers start: 52 outliers final: 38 residues processed: 148 average time/residue: 0.0908 time to fit residues: 21.4235 Evaluate side-chains 142 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 202 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 94 optimal weight: 5.9990 chunk 44 optimal weight: 0.0670 chunk 112 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1232 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.209202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.184333 restraints weight = 28033.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.182358 restraints weight = 48077.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.178835 restraints weight = 20178.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.179406 restraints weight = 15048.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.179783 restraints weight = 8930.441| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4157 r_free = 0.4157 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4157 r_free = 0.4157 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13575 Z= 0.134 Angle : 0.619 8.968 18484 Z= 0.308 Chirality : 0.042 0.244 2152 Planarity : 0.005 0.144 2226 Dihedral : 7.353 65.325 1946 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.35 % Allowed : 20.92 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.21), residues: 1620 helix: 1.26 (0.18), residues: 793 sheet: -0.44 (0.31), residues: 297 loop : -1.67 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.000 ARG A 148 TYR 0.022 0.001 TYR A 510 PHE 0.024 0.001 PHE A 994 TRP 0.011 0.001 TRP B 102 HIS 0.002 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (13565) covalent geometry : angle 0.61391 / 0.31 (18463) SS BOND : bond 0.00414 / 0.24 ( 6) SS BOND : angle 0.77097 / 0.50 ( 12) hydrogen bonds : bond 0.04674 / 3.10 ( 703) hydrogen bonds : angle 4.31004 / 3.16 ( 2030) Misc. bond : bond 0.00454 / 0.30 ( 1) link_NAG-ASN : bond 0.00698 / 0.49 ( 3) link_NAG-ASN : angle 3.67333 / 1.76 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7697 (ttp) cc_final: 0.7399 (ttp) REVERT: A 314 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7860 (m-10) REVERT: A 440 MET cc_start: 0.4309 (mmt) cc_final: 0.4015 (mmt) REVERT: A 443 LEU cc_start: 0.5846 (OUTLIER) cc_final: 0.5587 (mp) REVERT: A 497 MET cc_start: 0.3902 (mmm) cc_final: 0.3588 (mpp) REVERT: A 850 SER cc_start: 0.8274 (t) cc_final: 0.8034 (t) REVERT: A 953 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6606 (t80) REVERT: A 1010 MET cc_start: 0.6816 (tmm) cc_final: 0.6571 (tmm) REVERT: C 182 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7175 (p0) outliers start: 44 outliers final: 34 residues processed: 139 average time/residue: 0.0946 time to fit residues: 20.9308 Evaluate side-chains 139 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 202 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 155 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 ASN B 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.209161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.183300 restraints weight = 26793.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.181675 restraints weight = 50048.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.178305 restraints weight = 21040.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.178867 restraints weight = 15469.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.179067 restraints weight = 9616.915| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4157 r_free = 0.4157 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4157 r_free = 0.4157 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13575 Z= 0.133 Angle : 0.612 9.035 18484 Z= 0.305 Chirality : 0.041 0.203 2152 Planarity : 0.005 0.131 2226 Dihedral : 7.209 65.797 1946 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.21 % Allowed : 21.65 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.21), residues: 1620 helix: 1.33 (0.19), residues: 793 sheet: -0.43 (0.31), residues: 301 loop : -1.58 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG A 148 TYR 0.014 0.001 TYR A 953 PHE 0.025 0.001 PHE A 994 TRP 0.012 0.001 TRP B 102 HIS 0.002 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (13565) covalent geometry : angle 0.60754 / 0.30 (18463) SS BOND : bond 0.00529 / 0.32 ( 6) SS BOND : angle 0.90046 / 0.59 ( 12) hydrogen bonds : bond 0.04581 / 3.05 ( 703) hydrogen bonds : angle 4.27650 / 3.14 ( 2030) Misc. bond : bond 0.00390 / 0.26 ( 1) link_NAG-ASN : bond 0.00710 / 0.49 ( 3) link_NAG-ASN : angle 3.46103 / 1.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 106 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7144 (mmm) cc_final: 0.6817 (mmm) REVERT: A 75 MET cc_start: 0.7661 (ttp) cc_final: 0.7377 (ttp) REVERT: A 314 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7927 (m-10) REVERT: A 443 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5479 (mp) REVERT: A 468 GLU cc_start: 0.5811 (tp30) cc_final: 0.5403 (pt0) REVERT: A 497 MET cc_start: 0.3837 (mmm) cc_final: 0.3554 (mpp) REVERT: A 628 MET cc_start: 0.0523 (ttm) cc_final: 0.0184 (ttm) REVERT: A 850 SER cc_start: 0.8244 (t) cc_final: 0.7970 (t) REVERT: A 953 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.6608 (t80) REVERT: A 1010 MET cc_start: 0.6858 (tmm) cc_final: 0.6620 (tmm) REVERT: A 1192 ARG cc_start: 0.5573 (mmm160) cc_final: 0.5324 (mmm160) REVERT: C 182 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7171 (p0) outliers start: 42 outliers final: 36 residues processed: 139 average time/residue: 0.0898 time to fit residues: 19.7867 Evaluate side-chains 140 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 202 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 134 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.208701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.170431 restraints weight = 32742.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.171686 restraints weight = 46402.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.171585 restraints weight = 15233.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.171913 restraints weight = 21410.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.172148 restraints weight = 11588.501| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3991 r_free = 0.3991 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3991 r_free = 0.3991 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13575 Z= 0.142 Angle : 0.631 9.157 18484 Z= 0.317 Chirality : 0.042 0.207 2152 Planarity : 0.005 0.125 2226 Dihedral : 7.194 65.790 1946 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.28 % Allowed : 21.79 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.21), residues: 1620 helix: 1.34 (0.18), residues: 793 sheet: -0.42 (0.31), residues: 301 loop : -1.54 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG A 148 TYR 0.014 0.001 TYR A 953 PHE 0.026 0.001 PHE A 994 TRP 0.012 0.001 TRP B 102 HIS 0.002 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (13565) covalent geometry : angle 0.62735 / 0.32 (18463) SS BOND : bond 0.00571 / 0.34 ( 6) SS BOND : angle 0.94274 / 0.62 ( 12) hydrogen bonds : bond 0.04657 / 3.08 ( 703) hydrogen bonds : angle 4.31385 / 3.16 ( 2030) Misc. bond : bond 0.00378 / 0.25 ( 1) link_NAG-ASN : bond 0.00633 / 0.44 ( 3) link_NAG-ASN : angle 3.21536 / 1.55 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7250 (mmm) cc_final: 0.6848 (mmm) REVERT: A 75 MET cc_start: 0.7699 (ttp) cc_final: 0.7441 (ttp) REVERT: A 314 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.8010 (m-10) REVERT: A 443 LEU cc_start: 0.5719 (OUTLIER) cc_final: 0.5378 (mp) REVERT: A 468 GLU cc_start: 0.6212 (tp30) cc_final: 0.5448 (pt0) REVERT: A 497 MET cc_start: 0.3844 (mmm) cc_final: 0.3580 (mpp) REVERT: A 850 SER cc_start: 0.8406 (t) cc_final: 0.8096 (t) REVERT: A 953 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.6596 (t80) REVERT: A 1010 MET cc_start: 0.6970 (tmm) cc_final: 0.6715 (tmm) REVERT: C 182 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7261 (p0) outliers start: 43 outliers final: 36 residues processed: 136 average time/residue: 0.0945 time to fit residues: 20.4991 Evaluate side-chains 140 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 102 TRP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 202 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 147 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 128 optimal weight: 0.1980 chunk 31 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 0.0470 chunk 120 optimal weight: 0.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.211323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.179158 restraints weight = 21500.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.180737 restraints weight = 40291.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.177226 restraints weight = 17765.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.177600 restraints weight = 20881.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.177617 restraints weight = 12838.492| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4165 r_free = 0.4165 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4165 r_free = 0.4165 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13575 Z= 0.116 Angle : 0.600 9.565 18484 Z= 0.298 Chirality : 0.041 0.218 2152 Planarity : 0.004 0.118 2226 Dihedral : 6.959 67.128 1946 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.70 % Allowed : 22.16 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.21), residues: 1620 helix: 1.49 (0.19), residues: 795 sheet: -0.28 (0.32), residues: 296 loop : -1.47 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 148 TYR 0.014 0.001 TYR A 510 PHE 0.025 0.001 PHE A 994 TRP 0.010 0.001 TRP A 232 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (13565) covalent geometry : angle 0.59649 / 0.30 (18463) SS BOND : bond 0.00437 / 0.26 ( 6) SS BOND : angle 0.80167 / 0.51 ( 12) hydrogen bonds : bond 0.04268 / 2.82 ( 703) hydrogen bonds : angle 4.15979 / 3.05 ( 2030) Misc. bond : bond 0.00343 / 0.23 ( 1) link_NAG-ASN : bond 0.00551 / 0.39 ( 3) link_NAG-ASN : angle 3.06042 / 1.46 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2198.55 seconds wall clock time: 39 minutes 1.77 seconds (2341.77 seconds total)