Starting phenix.real_space_refine on Wed Jun 11 12:27:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7whv_32512/06_2025/7whv_32512.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whv_32512/06_2025/7whv_32512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7whv_32512/06_2025/7whv_32512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whv_32512/06_2025/7whv_32512.map" model { file = "/net/cci-nas-00/data/ceres_data/7whv_32512/06_2025/7whv_32512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whv_32512/06_2025/7whv_32512.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 60 5.16 5 Be 1 3.05 5 C 7953 2.51 5 N 2033 2.21 5 O 2278 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12331 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1158, 9249 Classifications: {'peptide': 1158} Link IDs: {'PTRANS': 39, 'TRANS': 1118} Chain breaks: 3 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2934 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 109 Unusual residues: {' MG': 1, '6PL': 2, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.78, per 1000 atoms: 0.63 Number of scatterers: 12331 At special positions: 0 Unit cell: (150.87, 97.37, 132.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 60 16.00 P 2 15.00 Mg 1 11.99 F 3 9.00 O 2278 8.00 N 2033 7.00 C 7953 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.02 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.01 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN B 240 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2848 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 11 sheets defined 44.1% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.665A pdb=" N VAL A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 244 through 274 removed outlier: 3.809A pdb=" N ARG A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 Processing helix chain 'A' and resid 452 through 456 removed outlier: 4.419A pdb=" N THR A 455 " --> pdb=" O CYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 464 removed outlier: 3.772A pdb=" N ARG A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 543 through 576 removed outlier: 4.272A pdb=" N ASN A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE A 551 " --> pdb=" O ARG A 547 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.523A pdb=" N ILE A 607 " --> pdb=" O TRP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 613 Processing helix chain 'A' and resid 615 through 634 removed outlier: 4.647A pdb=" N ILE A 619 " --> pdb=" O ILE A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 639 removed outlier: 3.774A pdb=" N LEU A 638 " --> pdb=" O ASP A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 659 Processing helix chain 'A' and resid 708 through 725 Processing helix chain 'A' and resid 762 through 777 removed outlier: 3.546A pdb=" N MET A 771 " --> pdb=" O CYS A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 811 Processing helix chain 'A' and resid 892 through 906 Processing helix chain 'A' and resid 921 through 936 removed outlier: 3.690A pdb=" N ALA A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 952 removed outlier: 3.614A pdb=" N ALA A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A 951 " --> pdb=" O VAL A 947 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 952 " --> pdb=" O ALA A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 981 Processing helix chain 'A' and resid 992 through 1003 Processing helix chain 'A' and resid 1035 through 1048 removed outlier: 3.564A pdb=" N LYS A1039 " --> pdb=" O ALA A1035 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A1046 " --> pdb=" O LYS A1042 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1060 Processing helix chain 'A' and resid 1074 through 1080 removed outlier: 3.778A pdb=" N LEU A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1097 removed outlier: 3.691A pdb=" N LYS A1089 " --> pdb=" O ASP A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1121 Processing helix chain 'A' and resid 1131 through 1133 No H-bonds generated for 'chain 'A' and resid 1131 through 1133' Processing helix chain 'A' and resid 1134 through 1141 Processing helix chain 'A' and resid 1153 through 1158 Processing helix chain 'A' and resid 1167 through 1174 removed outlier: 4.302A pdb=" N ARG A1171 " --> pdb=" O ARG A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1200 Proline residue: A1189 - end of helix removed outlier: 4.359A pdb=" N PHE A1198 " --> pdb=" O LYS A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1205 Processing helix chain 'A' and resid 1218 through 1225 Processing helix chain 'A' and resid 1230 through 1239 removed outlier: 4.258A pdb=" N VAL A1234 " --> pdb=" O THR A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1252 Processing helix chain 'A' and resid 1253 through 1255 No H-bonds generated for 'chain 'A' and resid 1253 through 1255' Processing helix chain 'A' and resid 1256 through 1261 Processing helix chain 'A' and resid 1266 through 1293 Proline residue: A1288 - end of helix Processing helix chain 'A' and resid 1307 through 1330 removed outlier: 3.698A pdb=" N TYR A1326 " --> pdb=" O SER A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1357 removed outlier: 3.551A pdb=" N SER A1345 " --> pdb=" O PHE A1341 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A1349 " --> pdb=" O SER A1345 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE A1350 " --> pdb=" O CYS A1346 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A1353 " --> pdb=" O VAL A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1363 removed outlier: 6.659A pdb=" N ALA A1361 " --> pdb=" O SER A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1372 Processing helix chain 'A' and resid 1375 through 1404 removed outlier: 3.871A pdb=" N TRP A1379 " --> pdb=" O ALA A1375 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A1383 " --> pdb=" O TRP A1379 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A1384 " --> pdb=" O ALA A1380 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A1387 " --> pdb=" O PHE A1383 " (cutoff:3.500A) Proline residue: A1392 - end of helix removed outlier: 3.500A pdb=" N PHE A1403 " --> pdb=" O PHE A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1418 Processing helix chain 'B' and resid 71 through 99 Proline residue: B 77 - end of helix removed outlier: 3.825A pdb=" N LYS B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 114 removed outlier: 3.619A pdb=" N ALA B 114 " --> pdb=" O CYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.880A pdb=" N LEU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 231 through 237 removed outlier: 4.377A pdb=" N ALA B 235 " --> pdb=" O CYS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 removed outlier: 4.118A pdb=" N ARG B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.559A pdb=" N GLU B 290 " --> pdb=" O PRO B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 350 through 354 Processing helix chain 'B' and resid 372 through 399 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 172 Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 280 Processing sheet with id=AA3, first strand: chain 'A' and resid 406 through 410 removed outlier: 6.531A pdb=" N TRP A 517 " --> pdb=" O THR A 424 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR A 424 " --> pdb=" O TRP A 517 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N MET A 519 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP A 418 " --> pdb=" O MET A 523 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 430 through 434 Processing sheet with id=AA5, first strand: chain 'A' and resid 1011 through 1014 removed outlier: 3.785A pdb=" N ALA A1099 " --> pdb=" O TYR A1068 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU A 985 " --> pdb=" O VAL A1100 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N CYS A1102 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A 987 " --> pdb=" O CYS A1102 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU A 662 " --> pdb=" O LYS A 984 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N TRP A 986 " --> pdb=" O GLU A 662 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE A 664 " --> pdb=" O TRP A 986 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU A 988 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 687 through 689 removed outlier: 7.003A pdb=" N ARG A 966 " --> pdb=" O GLN A 674 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL A 676 " --> pdb=" O GLU A 964 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU A 964 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU A 678 " --> pdb=" O ALA A 962 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA A 962 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 9.340A pdb=" N LYS A 680 " --> pdb=" O GLY A 960 " (cutoff:3.500A) removed outlier: 11.795A pdb=" N GLY A 960 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 10.108A pdb=" N CYS A 682 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 11.613A pdb=" N LEU A 958 " --> pdb=" O CYS A 682 " (cutoff:3.500A) removed outlier: 11.199A pdb=" N ILE A 684 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 13.879A pdb=" N ILE A 956 " --> pdb=" O ILE A 684 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE A 913 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY A 960 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU A 911 " --> pdb=" O GLY A 960 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA A 962 " --> pdb=" O ARG A 909 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ARG A 909 " --> pdb=" O ALA A 962 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER A 850 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE A 839 " --> pdb=" O SER A 850 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 852 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU A 835 " --> pdb=" O LYS A 854 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 830 " --> pdb=" O MET A 827 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY A 822 " --> pdb=" O LYS A 818 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LYS A 818 " --> pdb=" O GLY A 822 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE A 824 " --> pdb=" O VAL A 816 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 781 through 784 Processing sheet with id=AA8, first strand: chain 'A' and resid 1128 through 1129 removed outlier: 3.629A pdb=" N ILE A1147 " --> pdb=" O GLY A1129 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLY A1146 " --> pdb=" O ILE A1163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 126 through 129 removed outlier: 6.219A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU B 179 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N THR B 324 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 119 through 120 removed outlier: 5.841A pdb=" N ASP B 343 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLN B 246 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 227 through 228 removed outlier: 6.121A pdb=" N ILE B 227 " --> pdb=" O ALA B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 517 hydrogen bonds defined for protein. 1461 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: 6.26 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2113 1.31 - 1.44: 3404 1.44 - 1.56: 6999 1.56 - 1.68: 5 1.68 - 1.81: 92 Bond restraints: 12613 Sorted by residual: bond pdb=" F3 BEF A1602 " pdb="BE BEF A1602 " ideal model delta sigma weight residual 1.476 1.757 -0.281 2.00e-02 2.50e+03 1.98e+02 bond pdb=" F2 BEF A1602 " pdb="BE BEF A1602 " ideal model delta sigma weight residual 1.476 1.754 -0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" F1 BEF A1602 " pdb="BE BEF A1602 " ideal model delta sigma weight residual 1.476 1.745 -0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.326 0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" CG1 ILE A1321 " pdb=" CD1 ILE A1321 " ideal model delta sigma weight residual 1.513 1.362 0.151 3.90e-02 6.57e+02 1.51e+01 ... (remaining 12608 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 16121 2.53 - 5.05: 819 5.05 - 7.58: 117 7.58 - 10.10: 24 10.10 - 12.63: 8 Bond angle restraints: 17089 Sorted by residual: angle pdb=" N ILE A 706 " pdb=" CA ILE A 706 " pdb=" C ILE A 706 " ideal model delta sigma weight residual 112.29 105.60 6.69 9.40e-01 1.13e+00 5.07e+01 angle pdb=" C TYR B 229 " pdb=" N PRO B 230 " pdb=" CA PRO B 230 " ideal model delta sigma weight residual 119.84 111.34 8.50 1.25e+00 6.40e-01 4.63e+01 angle pdb=" CA TRP A 398 " pdb=" CB TRP A 398 " pdb=" CG TRP A 398 " ideal model delta sigma weight residual 113.60 126.23 -12.63 1.90e+00 2.77e-01 4.42e+01 angle pdb=" C ASN B 279 " pdb=" N TYR B 280 " pdb=" CA TYR B 280 " ideal model delta sigma weight residual 126.86 135.51 -8.65 1.57e+00 4.06e-01 3.03e+01 angle pdb=" N ILE B 403 " pdb=" CA ILE B 403 " pdb=" C ILE B 403 " ideal model delta sigma weight residual 111.91 107.33 4.58 8.90e-01 1.26e+00 2.65e+01 ... (remaining 17084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.58: 7298 22.58 - 45.16: 221 45.16 - 67.74: 25 67.74 - 90.32: 6 90.32 - 112.90: 4 Dihedral angle restraints: 7554 sinusoidal: 3116 harmonic: 4438 Sorted by residual: dihedral pdb=" CA ASN B 240 " pdb=" C ASN B 240 " pdb=" N ASP B 241 " pdb=" CA ASP B 241 " ideal model delta harmonic sigma weight residual -180.00 -145.93 -34.07 0 5.00e+00 4.00e-02 4.64e+01 dihedral pdb=" CA ASN B 279 " pdb=" C ASN B 279 " pdb=" N TYR B 280 " pdb=" CA TYR B 280 " ideal model delta harmonic sigma weight residual -180.00 -149.10 -30.90 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA PHE A1365 " pdb=" C PHE A1365 " pdb=" N PHE A1366 " pdb=" CA PHE A1366 " ideal model delta harmonic sigma weight residual -180.00 -149.80 -30.20 0 5.00e+00 4.00e-02 3.65e+01 ... (remaining 7551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1662 0.116 - 0.231: 213 0.231 - 0.346: 10 0.346 - 0.462: 4 0.462 - 0.577: 2 Chirality restraints: 1891 Sorted by residual: chirality pdb=" CG LEU A1126 " pdb=" CB LEU A1126 " pdb=" CD1 LEU A1126 " pdb=" CD2 LEU A1126 " both_signs ideal model delta sigma weight residual False -2.59 -2.01 -0.58 2.00e-01 2.50e+01 8.33e+00 chirality pdb=" CB ILE B 359 " pdb=" CA ILE B 359 " pdb=" CG1 ILE B 359 " pdb=" CG2 ILE B 359 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" C2 NAG C 1 " pdb=" C1 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" N2 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.06 -0.44 2.00e-01 2.50e+01 4.76e+00 ... (remaining 1888 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 142 " 0.050 2.00e-02 2.50e+03 4.04e-02 4.08e+01 pdb=" CG TRP B 142 " -0.106 2.00e-02 2.50e+03 pdb=" CD1 TRP B 142 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP B 142 " -0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP B 142 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 142 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 142 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 142 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 142 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 142 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 398 " -0.079 2.00e-02 2.50e+03 3.87e-02 3.75e+01 pdb=" CG TRP A 398 " 0.082 2.00e-02 2.50e+03 pdb=" CD1 TRP A 398 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP A 398 " 0.029 2.00e-02 2.50e+03 pdb=" NE1 TRP A 398 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 398 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 398 " 0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 398 " -0.027 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 398 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 398 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " 0.029 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" C PHE B 398 " -0.099 2.00e-02 2.50e+03 pdb=" O PHE B 398 " 0.037 2.00e-02 2.50e+03 pdb=" N GLY B 399 " 0.033 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 308 2.66 - 3.22: 11659 3.22 - 3.78: 21253 3.78 - 4.34: 29104 4.34 - 4.90: 46479 Nonbonded interactions: 108803 Sorted by model distance: nonbonded pdb=" OD1 ASP A 667 " pdb="MG MG A1601 " model vdw 2.100 2.170 nonbonded pdb=" OD2 ASP A 667 " pdb=" F1 BEF A1602 " model vdw 2.123 2.990 nonbonded pdb=" OD1 ASP A1130 " pdb=" F1 BEF A1602 " model vdw 2.141 2.990 nonbonded pdb=" O THR A 669 " pdb=" F1 BEF A1602 " model vdw 2.175 2.990 nonbonded pdb=" O THR A1353 " pdb=" OG SER A1357 " model vdw 2.246 3.040 ... (remaining 108798 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 41.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.980 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 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 : 0.016 0.281 12619 Z= 0.680 Angle : 1.304 12.880 17102 Z= 0.704 Chirality : 0.079 0.577 1891 Planarity : 0.009 0.061 2159 Dihedral : 12.087 112.895 4700 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.02 % Favored : 92.91 % Rotamer: Outliers : 0.60 % Allowed : 3.25 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.17), residues: 1510 helix: -3.44 (0.13), residues: 601 sheet: -2.01 (0.30), residues: 192 loop : -1.94 (0.21), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.007 TRP B 142 HIS 0.013 0.005 HIS B 186 PHE 0.060 0.006 PHE B 243 TYR 0.046 0.006 TYR B 297 ARG 0.018 0.002 ARG A 880 Details of bonding type rmsd link_NAG-ASN : bond 0.02665 ( 1) link_NAG-ASN : angle 5.67714 ( 3) link_BETA1-4 : bond 0.04099 ( 2) link_BETA1-4 : angle 7.46080 ( 6) hydrogen bonds : bond 0.24877 ( 517) hydrogen bonds : angle 9.69829 ( 1461) SS BOND : bond 0.01678 ( 2) SS BOND : angle 2.93040 ( 4) covalent geometry : bond 0.01599 (12613) covalent geometry : angle 1.29389 (17089) Misc. bond : bond 0.00556 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 269 time to evaluate : 1.527 Fit side-chains REVERT: A 464 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7598 (mtm180) REVERT: A 599 PHE cc_start: 0.7186 (t80) cc_final: 0.6929 (t80) REVERT: A 674 GLN cc_start: 0.8053 (tt0) cc_final: 0.7789 (tt0) REVERT: A 685 ASN cc_start: 0.7522 (t160) cc_final: 0.7244 (t0) REVERT: A 715 GLU cc_start: 0.7173 (tp30) cc_final: 0.6972 (tp30) REVERT: A 765 ARG cc_start: 0.6869 (mmp-170) cc_final: 0.6516 (mmp80) REVERT: A 782 VAL cc_start: 0.7695 (t) cc_final: 0.7416 (m) REVERT: A 824 ILE cc_start: 0.8091 (mt) cc_final: 0.7761 (mp) REVERT: A 827 MET cc_start: 0.7069 (mtp) cc_final: 0.6835 (mtp) REVERT: A 835 GLU cc_start: 0.7539 (tt0) cc_final: 0.7314 (tt0) REVERT: A 837 LEU cc_start: 0.8227 (mt) cc_final: 0.8008 (mp) REVERT: A 840 LEU cc_start: 0.8587 (mt) cc_final: 0.8354 (mt) REVERT: A 847 LYS cc_start: 0.7603 (mttp) cc_final: 0.7351 (mtpm) REVERT: A 853 VAL cc_start: 0.8101 (m) cc_final: 0.7720 (p) REVERT: A 854 LYS cc_start: 0.7406 (tttt) cc_final: 0.7066 (ttpp) REVERT: A 898 LEU cc_start: 0.8011 (tp) cc_final: 0.7748 (tp) REVERT: A 973 ASP cc_start: 0.7238 (m-30) cc_final: 0.6958 (m-30) REVERT: A 1222 MET cc_start: 0.8115 (mtp) cc_final: 0.7798 (mtp) REVERT: B 54 LYS cc_start: 0.7665 (ttpt) cc_final: 0.7399 (mmtm) REVERT: B 134 LYS cc_start: 0.7948 (mttt) cc_final: 0.7700 (mttt) REVERT: B 215 ASN cc_start: 0.8368 (p0) cc_final: 0.8116 (p0) REVERT: B 290 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6809 (mm-30) REVERT: B 315 MET cc_start: 0.8712 (mmm) cc_final: 0.8277 (mmm) outliers start: 8 outliers final: 3 residues processed: 277 average time/residue: 1.3033 time to fit residues: 395.8578 Evaluate side-chains 166 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 163 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 chunk 45 optimal weight: 0.0770 chunk 71 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 410 HIS A 411 ASN A 437 ASN A 443 ASN A 475 HIS A 477 ASN A 497 ASN A 556 ASN ** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 ASN A 939 ASN A1004 ASN A1061 HIS A1067 ASN A1176 HIS A1266 ASN A1307 HIS ** A1330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 ASN B 155 GLN B 255 ASN B 256 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.159899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.132117 restraints weight = 15046.155| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.54 r_work: 0.3424 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12619 Z= 0.182 Angle : 0.714 11.631 17102 Z= 0.374 Chirality : 0.047 0.324 1891 Planarity : 0.005 0.050 2159 Dihedral : 9.206 63.936 1822 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.47 % Allowed : 9.67 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.19), residues: 1510 helix: -1.54 (0.17), residues: 624 sheet: -1.66 (0.32), residues: 193 loop : -1.48 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 142 HIS 0.005 0.001 HIS A1330 PHE 0.021 0.002 PHE A 206 TYR 0.024 0.002 TYR A1289 ARG 0.007 0.001 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.01219 ( 1) link_NAG-ASN : angle 4.92002 ( 3) link_BETA1-4 : bond 0.00600 ( 2) link_BETA1-4 : angle 4.42544 ( 6) hydrogen bonds : bond 0.04784 ( 517) hydrogen bonds : angle 5.85245 ( 1461) SS BOND : bond 0.00494 ( 2) SS BOND : angle 1.34320 ( 4) covalent geometry : bond 0.00412 (12613) covalent geometry : angle 0.70566 (17089) Misc. bond : bond 0.00215 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 192 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: A 455 THR cc_start: 0.7717 (p) cc_final: 0.7500 (m) REVERT: A 561 PHE cc_start: 0.8075 (t80) cc_final: 0.7856 (t80) REVERT: A 574 TYR cc_start: 0.7690 (t80) cc_final: 0.7420 (t80) REVERT: A 674 GLN cc_start: 0.8389 (tt0) cc_final: 0.8082 (tt0) REVERT: A 677 MET cc_start: 0.8267 (tpp) cc_final: 0.8063 (tpp) REVERT: A 715 GLU cc_start: 0.7624 (tp30) cc_final: 0.7217 (tp30) REVERT: A 765 ARG cc_start: 0.6895 (mmp-170) cc_final: 0.6607 (mmp80) REVERT: A 768 GLU cc_start: 0.7315 (mt-10) cc_final: 0.7068 (mt-10) REVERT: A 824 ILE cc_start: 0.8007 (mt) cc_final: 0.7740 (mp) REVERT: A 827 MET cc_start: 0.7549 (mtp) cc_final: 0.7202 (mtp) REVERT: A 835 GLU cc_start: 0.7992 (tt0) cc_final: 0.7665 (tt0) REVERT: A 837 LEU cc_start: 0.7697 (mt) cc_final: 0.7456 (mp) REVERT: A 847 LYS cc_start: 0.7724 (mttp) cc_final: 0.7486 (mtpm) REVERT: A 913 ILE cc_start: 0.7879 (mm) cc_final: 0.7579 (tp) REVERT: A 973 ASP cc_start: 0.7895 (m-30) cc_final: 0.7651 (m-30) REVERT: A 1187 MET cc_start: 0.8349 (ttp) cc_final: 0.7708 (tmt) REVERT: A 1409 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7134 (tp30) REVERT: B 54 LYS cc_start: 0.8100 (ttpt) cc_final: 0.7452 (mmpt) REVERT: B 80 LEU cc_start: 0.7781 (mt) cc_final: 0.7367 (tp) REVERT: B 96 GLN cc_start: 0.7541 (mp-120) cc_final: 0.6658 (tt0) REVERT: B 134 LYS cc_start: 0.7977 (mttt) cc_final: 0.7631 (mttt) REVERT: B 215 ASN cc_start: 0.8332 (p0) cc_final: 0.8054 (p0) REVERT: B 307 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6893 (p0) REVERT: B 315 MET cc_start: 0.8845 (mmm) cc_final: 0.8545 (mmm) REVERT: B 334 THR cc_start: 0.7597 (OUTLIER) cc_final: 0.7360 (m) outliers start: 46 outliers final: 21 residues processed: 228 average time/residue: 1.1461 time to fit residues: 287.6573 Evaluate side-chains 178 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1194 LYS Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1398 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 403 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 chunk 80 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 134 optimal weight: 0.0040 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 0.2980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN A 556 ASN A 675 ASN ** A1330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN B 363 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.161226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.133433 restraints weight = 15012.797| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.56 r_work: 0.3450 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12619 Z= 0.142 Angle : 0.627 11.808 17102 Z= 0.325 Chirality : 0.045 0.345 1891 Planarity : 0.004 0.046 2159 Dihedral : 7.868 54.404 1822 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.17 % Allowed : 11.71 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.21), residues: 1510 helix: -0.52 (0.20), residues: 628 sheet: -1.40 (0.34), residues: 195 loop : -1.28 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 142 HIS 0.007 0.001 HIS A1330 PHE 0.018 0.002 PHE A1198 TYR 0.028 0.002 TYR A 172 ARG 0.007 0.000 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00986 ( 1) link_NAG-ASN : angle 5.08608 ( 3) link_BETA1-4 : bond 0.00390 ( 2) link_BETA1-4 : angle 4.16916 ( 6) hydrogen bonds : bond 0.04132 ( 517) hydrogen bonds : angle 5.38021 ( 1461) SS BOND : bond 0.00266 ( 2) SS BOND : angle 1.04471 ( 4) covalent geometry : bond 0.00321 (12613) covalent geometry : angle 0.61866 (17089) Misc. bond : bond 0.00264 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 1.381 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6831 (tmt) REVERT: A 574 TYR cc_start: 0.7724 (t80) cc_final: 0.7451 (t80) REVERT: A 642 LYS cc_start: 0.8488 (tttt) cc_final: 0.8037 (ttpt) REVERT: A 674 GLN cc_start: 0.8376 (tt0) cc_final: 0.8128 (tt0) REVERT: A 715 GLU cc_start: 0.7610 (tp30) cc_final: 0.7230 (tt0) REVERT: A 765 ARG cc_start: 0.7125 (mmp-170) cc_final: 0.6780 (mmp80) REVERT: A 768 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6916 (mt-10) REVERT: A 792 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7708 (pp) REVERT: A 827 MET cc_start: 0.7546 (mtp) cc_final: 0.7283 (mtp) REVERT: A 835 GLU cc_start: 0.8051 (tt0) cc_final: 0.7639 (tt0) REVERT: A 840 LEU cc_start: 0.8581 (mt) cc_final: 0.7992 (mt) REVERT: A 847 LYS cc_start: 0.7734 (mttp) cc_final: 0.7492 (mtpm) REVERT: A 898 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7215 (mm) REVERT: A 973 ASP cc_start: 0.7877 (m-30) cc_final: 0.7626 (m-30) REVERT: A 1215 TYR cc_start: 0.8832 (m-80) cc_final: 0.8617 (m-80) REVERT: A 1409 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7080 (tp30) REVERT: B 54 LYS cc_start: 0.8069 (ttpt) cc_final: 0.7371 (mmpt) REVERT: B 80 LEU cc_start: 0.7711 (mt) cc_final: 0.7306 (tp) REVERT: B 96 GLN cc_start: 0.7508 (mp-120) cc_final: 0.6646 (tt0) REVERT: B 134 LYS cc_start: 0.7857 (mttt) cc_final: 0.7551 (mttt) REVERT: B 292 MET cc_start: 0.8383 (tpp) cc_final: 0.7118 (ttm) REVERT: B 307 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.6976 (p0) REVERT: B 315 MET cc_start: 0.8871 (mmm) cc_final: 0.8524 (mmm) REVERT: B 333 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7287 (p0) REVERT: B 334 THR cc_start: 0.7730 (t) cc_final: 0.7520 (m) outliers start: 42 outliers final: 14 residues processed: 203 average time/residue: 1.2236 time to fit residues: 271.7896 Evaluate side-chains 165 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 403 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 88 optimal weight: 0.0980 chunk 106 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1109 GLN A1195 ASN ** A1330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1416 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.159939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.131803 restraints weight = 14962.363| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.54 r_work: 0.3418 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12619 Z= 0.174 Angle : 0.642 11.822 17102 Z= 0.332 Chirality : 0.046 0.328 1891 Planarity : 0.004 0.052 2159 Dihedral : 7.736 58.562 1821 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.70 % Allowed : 12.99 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.21), residues: 1510 helix: -0.03 (0.20), residues: 625 sheet: -1.22 (0.35), residues: 191 loop : -1.18 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 314 HIS 0.004 0.001 HIS A 475 PHE 0.020 0.002 PHE A1198 TYR 0.027 0.002 TYR A 172 ARG 0.007 0.001 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.01372 ( 1) link_NAG-ASN : angle 5.06249 ( 3) link_BETA1-4 : bond 0.00674 ( 2) link_BETA1-4 : angle 4.09484 ( 6) hydrogen bonds : bond 0.04145 ( 517) hydrogen bonds : angle 5.24429 ( 1461) SS BOND : bond 0.00239 ( 2) SS BOND : angle 1.34739 ( 4) covalent geometry : bond 0.00402 (12613) covalent geometry : angle 0.63382 (17089) Misc. bond : bond 0.00185 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 158 time to evaluate : 1.372 Fit side-chains REVERT: A 189 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6812 (tmt) REVERT: A 574 TYR cc_start: 0.7745 (t80) cc_final: 0.7444 (t80) REVERT: A 642 LYS cc_start: 0.8498 (tttt) cc_final: 0.8059 (ttpt) REVERT: A 674 GLN cc_start: 0.8387 (tt0) cc_final: 0.8076 (tt0) REVERT: A 715 GLU cc_start: 0.7553 (tp30) cc_final: 0.7064 (tp30) REVERT: A 765 ARG cc_start: 0.7116 (mmp-170) cc_final: 0.6788 (mmp80) REVERT: A 768 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6927 (mt-10) REVERT: A 792 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7678 (pp) REVERT: A 801 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: A 827 MET cc_start: 0.7506 (mtp) cc_final: 0.7274 (mtp) REVERT: A 835 GLU cc_start: 0.7851 (tt0) cc_final: 0.7378 (tt0) REVERT: A 840 LEU cc_start: 0.8592 (mt) cc_final: 0.8146 (mt) REVERT: A 846 ARG cc_start: 0.6159 (mtp85) cc_final: 0.5920 (mtp180) REVERT: A 847 LYS cc_start: 0.7743 (mttp) cc_final: 0.7512 (mtpm) REVERT: A 898 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7207 (mm) REVERT: A 916 ARG cc_start: 0.6781 (ptm-80) cc_final: 0.6164 (mtm180) REVERT: A 973 ASP cc_start: 0.7946 (m-30) cc_final: 0.7688 (m-30) REVERT: A 1215 TYR cc_start: 0.8824 (m-80) cc_final: 0.8616 (m-80) REVERT: A 1409 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7140 (tp30) REVERT: A 1416 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7311 (mp10) REVERT: B 54 LYS cc_start: 0.8026 (ttpt) cc_final: 0.7321 (mmpt) REVERT: B 80 LEU cc_start: 0.7727 (mt) cc_final: 0.7316 (tp) REVERT: B 96 GLN cc_start: 0.7559 (mp-120) cc_final: 0.6678 (tt0) REVERT: B 134 LYS cc_start: 0.7885 (mttt) cc_final: 0.7574 (mttt) REVERT: B 196 ASP cc_start: 0.7876 (m-30) cc_final: 0.7477 (m-30) REVERT: B 307 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.7000 (p0) REVERT: B 333 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7427 (p0) outliers start: 49 outliers final: 23 residues processed: 190 average time/residue: 1.1935 time to fit residues: 248.7000 Evaluate side-chains 171 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 403 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 130 optimal weight: 0.0970 chunk 53 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 ASN A1109 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.160054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.131846 restraints weight = 14885.194| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.54 r_work: 0.3418 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12619 Z= 0.170 Angle : 0.628 11.843 17102 Z= 0.325 Chirality : 0.045 0.331 1891 Planarity : 0.004 0.055 2159 Dihedral : 7.711 59.920 1821 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.00 % Allowed : 13.52 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.21), residues: 1510 helix: 0.12 (0.21), residues: 628 sheet: -1.21 (0.34), residues: 199 loop : -1.13 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 314 HIS 0.003 0.001 HIS A 475 PHE 0.020 0.002 PHE A1198 TYR 0.029 0.002 TYR A 172 ARG 0.007 0.001 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.01345 ( 1) link_NAG-ASN : angle 5.09910 ( 3) link_BETA1-4 : bond 0.00683 ( 2) link_BETA1-4 : angle 3.89722 ( 6) hydrogen bonds : bond 0.04055 ( 517) hydrogen bonds : angle 5.16530 ( 1461) SS BOND : bond 0.00261 ( 2) SS BOND : angle 1.29915 ( 4) covalent geometry : bond 0.00394 (12613) covalent geometry : angle 0.62016 (17089) Misc. bond : bond 0.00189 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 155 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: A 574 TYR cc_start: 0.7827 (t80) cc_final: 0.7504 (t80) REVERT: A 674 GLN cc_start: 0.8399 (tt0) cc_final: 0.8194 (tt0) REVERT: A 715 GLU cc_start: 0.7550 (tp30) cc_final: 0.6974 (tp30) REVERT: A 765 ARG cc_start: 0.7105 (mmp-170) cc_final: 0.6784 (mmp80) REVERT: A 768 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6955 (mt-10) REVERT: A 792 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7667 (pp) REVERT: A 835 GLU cc_start: 0.7854 (tt0) cc_final: 0.7324 (tt0) REVERT: A 840 LEU cc_start: 0.8555 (mt) cc_final: 0.8206 (mt) REVERT: A 846 ARG cc_start: 0.6218 (mtp85) cc_final: 0.5894 (mtp180) REVERT: A 847 LYS cc_start: 0.7770 (mttp) cc_final: 0.7540 (mtpm) REVERT: A 854 LYS cc_start: 0.7089 (ttpp) cc_final: 0.6855 (ttpp) REVERT: A 898 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7189 (mm) REVERT: A 913 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.8000 (tt) REVERT: A 973 ASP cc_start: 0.7957 (m-30) cc_final: 0.7705 (m-30) REVERT: A 1151 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7702 (pm20) REVERT: A 1215 TYR cc_start: 0.8848 (m-80) cc_final: 0.8641 (m-80) REVERT: A 1409 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7077 (tp30) REVERT: A 1416 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7375 (mp10) REVERT: B 54 LYS cc_start: 0.8060 (ttpt) cc_final: 0.7316 (mmpt) REVERT: B 80 LEU cc_start: 0.7742 (mt) cc_final: 0.7341 (tp) REVERT: B 96 GLN cc_start: 0.7588 (mp-120) cc_final: 0.6705 (tt0) REVERT: B 134 LYS cc_start: 0.7940 (mttt) cc_final: 0.7594 (mttt) REVERT: B 196 ASP cc_start: 0.7873 (m-30) cc_final: 0.7497 (m-30) REVERT: B 292 MET cc_start: 0.8387 (tpp) cc_final: 0.7140 (ttm) REVERT: B 307 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.7111 (p0) REVERT: B 333 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7445 (p0) outliers start: 53 outliers final: 30 residues processed: 195 average time/residue: 1.2332 time to fit residues: 263.6554 Evaluate side-chains 179 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 348 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 56 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 147 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1109 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.159720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.131500 restraints weight = 15109.318| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.55 r_work: 0.3416 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12619 Z= 0.174 Angle : 0.633 11.869 17102 Z= 0.327 Chirality : 0.045 0.334 1891 Planarity : 0.004 0.056 2159 Dihedral : 7.663 59.981 1821 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.23 % Allowed : 14.05 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.21), residues: 1510 helix: 0.22 (0.21), residues: 631 sheet: -1.18 (0.34), residues: 199 loop : -1.18 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 314 HIS 0.003 0.001 HIS B 347 PHE 0.020 0.002 PHE A1198 TYR 0.030 0.002 TYR A 172 ARG 0.008 0.000 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.01378 ( 1) link_NAG-ASN : angle 5.14222 ( 3) link_BETA1-4 : bond 0.00654 ( 2) link_BETA1-4 : angle 3.83468 ( 6) hydrogen bonds : bond 0.04055 ( 517) hydrogen bonds : angle 5.12581 ( 1461) SS BOND : bond 0.00262 ( 2) SS BOND : angle 1.33043 ( 4) covalent geometry : bond 0.00404 (12613) covalent geometry : angle 0.62540 (17089) Misc. bond : bond 0.00187 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 158 time to evaluate : 1.334 Fit side-chains REVERT: A 574 TYR cc_start: 0.7876 (t80) cc_final: 0.7538 (t80) REVERT: A 674 GLN cc_start: 0.8423 (tt0) cc_final: 0.8145 (tt0) REVERT: A 765 ARG cc_start: 0.7038 (mmp-170) cc_final: 0.6722 (mmp80) REVERT: A 768 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6939 (mt-10) REVERT: A 792 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7650 (pp) REVERT: A 835 GLU cc_start: 0.7766 (tt0) cc_final: 0.7274 (tt0) REVERT: A 840 LEU cc_start: 0.8575 (mt) cc_final: 0.8226 (mt) REVERT: A 846 ARG cc_start: 0.6175 (mtp85) cc_final: 0.5835 (mtp180) REVERT: A 847 LYS cc_start: 0.7770 (mttp) cc_final: 0.7523 (mtpm) REVERT: A 898 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7118 (mm) REVERT: A 916 ARG cc_start: 0.6768 (ptm-80) cc_final: 0.6151 (mtm180) REVERT: A 973 ASP cc_start: 0.7957 (m-30) cc_final: 0.7700 (m-30) REVERT: A 1036 LEU cc_start: 0.5726 (pt) cc_final: 0.5261 (OUTLIER) REVERT: A 1151 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7679 (pm20) REVERT: A 1215 TYR cc_start: 0.8825 (m-80) cc_final: 0.8612 (m-80) REVERT: A 1409 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7055 (tp30) REVERT: B 54 LYS cc_start: 0.8050 (ttpt) cc_final: 0.7286 (mmtm) REVERT: B 80 LEU cc_start: 0.7731 (mt) cc_final: 0.7331 (tp) REVERT: B 96 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.6691 (tt0) REVERT: B 134 LYS cc_start: 0.7924 (mttt) cc_final: 0.7574 (mttt) REVERT: B 196 ASP cc_start: 0.7858 (m-30) cc_final: 0.7481 (m-30) REVERT: B 275 LYS cc_start: 0.7405 (tttp) cc_final: 0.7098 (tptt) REVERT: B 292 MET cc_start: 0.8389 (tpp) cc_final: 0.7131 (ttm) REVERT: B 307 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7114 (p0) REVERT: B 333 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7444 (p0) outliers start: 56 outliers final: 29 residues processed: 196 average time/residue: 1.1574 time to fit residues: 248.6491 Evaluate side-chains 179 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 334 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 132 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 120 optimal weight: 0.7980 chunk 138 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 130 optimal weight: 0.0370 chunk 33 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 139 optimal weight: 0.0970 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1109 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.162146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134217 restraints weight = 14915.309| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.64 r_work: 0.3445 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12619 Z= 0.133 Angle : 0.599 11.812 17102 Z= 0.309 Chirality : 0.044 0.358 1891 Planarity : 0.003 0.057 2159 Dihedral : 7.307 56.504 1819 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.93 % Allowed : 14.50 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.21), residues: 1510 helix: 0.37 (0.21), residues: 628 sheet: -1.00 (0.35), residues: 193 loop : -1.13 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1352 HIS 0.003 0.001 HIS A 475 PHE 0.017 0.002 PHE A1198 TYR 0.030 0.002 TYR A 172 ARG 0.010 0.000 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.01038 ( 1) link_NAG-ASN : angle 5.21308 ( 3) link_BETA1-4 : bond 0.00449 ( 2) link_BETA1-4 : angle 3.54369 ( 6) hydrogen bonds : bond 0.03778 ( 517) hydrogen bonds : angle 4.98688 ( 1461) SS BOND : bond 0.00177 ( 2) SS BOND : angle 1.08155 ( 4) covalent geometry : bond 0.00300 (12613) covalent geometry : angle 0.59173 (17089) Misc. bond : bond 0.00211 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 156 time to evaluate : 1.433 Fit side-chains revert: symmetry clash REVERT: A 470 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7164 (pt0) REVERT: A 574 TYR cc_start: 0.7840 (t80) cc_final: 0.7482 (t80) REVERT: A 603 TRP cc_start: 0.7621 (m100) cc_final: 0.7216 (m-10) REVERT: A 674 GLN cc_start: 0.8321 (tt0) cc_final: 0.8093 (tt0) REVERT: A 765 ARG cc_start: 0.7043 (mmp-170) cc_final: 0.6729 (mmp80) REVERT: A 768 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6849 (mt-10) REVERT: A 792 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7646 (pp) REVERT: A 835 GLU cc_start: 0.7493 (tt0) cc_final: 0.7150 (mt-10) REVERT: A 847 LYS cc_start: 0.7797 (mttp) cc_final: 0.7533 (mtpm) REVERT: A 894 GLU cc_start: 0.5989 (mp0) cc_final: 0.5789 (mp0) REVERT: A 898 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7067 (mm) REVERT: A 1036 LEU cc_start: 0.5822 (pt) cc_final: 0.5409 (pp) REVERT: A 1151 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7346 (pm20) REVERT: A 1409 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7004 (tp30) REVERT: B 54 LYS cc_start: 0.8023 (ttpt) cc_final: 0.7272 (mmpt) REVERT: B 80 LEU cc_start: 0.7754 (mt) cc_final: 0.7344 (tp) REVERT: B 96 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.6669 (tt0) REVERT: B 134 LYS cc_start: 0.7890 (mttt) cc_final: 0.7590 (mttt) REVERT: B 138 THR cc_start: 0.7321 (p) cc_final: 0.6817 (t) REVERT: B 196 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7365 (m-30) REVERT: B 292 MET cc_start: 0.8447 (tpp) cc_final: 0.7304 (ttm) REVERT: B 307 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7154 (p0) REVERT: B 333 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7386 (p0) REVERT: B 388 MET cc_start: 0.6711 (mmp) cc_final: 0.6233 (mmt) outliers start: 52 outliers final: 20 residues processed: 192 average time/residue: 1.2082 time to fit residues: 254.1173 Evaluate side-chains 167 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 334 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 77 optimal weight: 0.4980 chunk 125 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 99 optimal weight: 0.4980 chunk 110 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1109 GLN A1266 ASN A1416 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.159565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.131269 restraints weight = 15081.665| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.53 r_work: 0.3410 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 12619 Z= 0.180 Angle : 0.640 12.009 17102 Z= 0.329 Chirality : 0.045 0.325 1891 Planarity : 0.004 0.060 2159 Dihedral : 7.427 56.228 1819 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.25 % Allowed : 15.79 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.21), residues: 1510 helix: 0.38 (0.21), residues: 627 sheet: -1.06 (0.34), residues: 199 loop : -1.14 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 314 HIS 0.006 0.001 HIS A 475 PHE 0.021 0.002 PHE A1198 TYR 0.032 0.002 TYR A 172 ARG 0.009 0.001 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.01393 ( 1) link_NAG-ASN : angle 5.11794 ( 3) link_BETA1-4 : bond 0.00771 ( 2) link_BETA1-4 : angle 3.78712 ( 6) hydrogen bonds : bond 0.04013 ( 517) hydrogen bonds : angle 5.04541 ( 1461) SS BOND : bond 0.00258 ( 2) SS BOND : angle 1.47903 ( 4) covalent geometry : bond 0.00417 (12613) covalent geometry : angle 0.63263 (17089) Misc. bond : bond 0.00203 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: A 470 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7077 (pt0) REVERT: A 574 TYR cc_start: 0.7907 (t80) cc_final: 0.7579 (t80) REVERT: A 603 TRP cc_start: 0.7655 (m100) cc_final: 0.7252 (m-10) REVERT: A 674 GLN cc_start: 0.8409 (tt0) cc_final: 0.8136 (tt0) REVERT: A 768 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6929 (mt-10) REVERT: A 792 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7664 (pp) REVERT: A 847 LYS cc_start: 0.7706 (mttp) cc_final: 0.7465 (mtpm) REVERT: A 898 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7126 (mm) REVERT: A 916 ARG cc_start: 0.6725 (ptm-80) cc_final: 0.6382 (mtm180) REVERT: A 973 ASP cc_start: 0.7978 (m-30) cc_final: 0.7713 (m-30) REVERT: A 1036 LEU cc_start: 0.5545 (pt) cc_final: 0.5185 (pp) REVERT: A 1151 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7361 (pm20) REVERT: A 1409 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7107 (tp30) REVERT: B 54 LYS cc_start: 0.8053 (ttpt) cc_final: 0.7353 (tptt) REVERT: B 80 LEU cc_start: 0.7781 (mt) cc_final: 0.7372 (tp) REVERT: B 96 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6763 (tt0) REVERT: B 134 LYS cc_start: 0.7770 (mttt) cc_final: 0.7531 (mttt) REVERT: B 196 ASP cc_start: 0.7844 (m-30) cc_final: 0.7447 (m-30) REVERT: B 275 LYS cc_start: 0.7420 (tttp) cc_final: 0.7122 (tptt) REVERT: B 292 MET cc_start: 0.8377 (tpp) cc_final: 0.7168 (ttm) REVERT: B 307 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7210 (p0) outliers start: 43 outliers final: 26 residues processed: 183 average time/residue: 1.1356 time to fit residues: 228.4547 Evaluate side-chains 176 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1398 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 334 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 77 optimal weight: 0.0170 chunk 83 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1109 GLN A1266 ASN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.159588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.131528 restraints weight = 14971.411| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.62 r_work: 0.3409 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12619 Z= 0.176 Angle : 0.639 12.369 17102 Z= 0.328 Chirality : 0.045 0.324 1891 Planarity : 0.004 0.062 2159 Dihedral : 7.410 57.940 1819 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.32 % Allowed : 15.94 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.21), residues: 1510 helix: 0.40 (0.21), residues: 628 sheet: -1.14 (0.34), residues: 209 loop : -1.14 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 314 HIS 0.006 0.001 HIS A 475 PHE 0.021 0.002 PHE A1198 TYR 0.034 0.002 TYR A 172 ARG 0.008 0.001 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.01333 ( 1) link_NAG-ASN : angle 5.18284 ( 3) link_BETA1-4 : bond 0.00623 ( 2) link_BETA1-4 : angle 3.67208 ( 6) hydrogen bonds : bond 0.03980 ( 517) hydrogen bonds : angle 5.03383 ( 1461) SS BOND : bond 0.00268 ( 2) SS BOND : angle 1.39860 ( 4) covalent geometry : bond 0.00410 (12613) covalent geometry : angle 0.63097 (17089) Misc. bond : bond 0.00199 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 1.248 Fit side-chains REVERT: A 470 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7060 (pt0) REVERT: A 574 TYR cc_start: 0.7905 (t80) cc_final: 0.7567 (t80) REVERT: A 603 TRP cc_start: 0.7650 (m100) cc_final: 0.7242 (m-10) REVERT: A 674 GLN cc_start: 0.8407 (tt0) cc_final: 0.8139 (tt0) REVERT: A 765 ARG cc_start: 0.7344 (tpp-160) cc_final: 0.6974 (mmp80) REVERT: A 768 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6930 (mt-10) REVERT: A 792 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7668 (pp) REVERT: A 835 GLU cc_start: 0.7411 (tt0) cc_final: 0.7086 (mt-10) REVERT: A 847 LYS cc_start: 0.7701 (mttp) cc_final: 0.7458 (mtpm) REVERT: A 898 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7118 (mm) REVERT: A 916 ARG cc_start: 0.6728 (ptm-80) cc_final: 0.6376 (mtm180) REVERT: A 1036 LEU cc_start: 0.5666 (pt) cc_final: 0.5319 (pp) REVERT: A 1151 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7389 (pm20) REVERT: A 1409 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7104 (tp30) REVERT: B 54 LYS cc_start: 0.8047 (ttpt) cc_final: 0.7345 (tptt) REVERT: B 80 LEU cc_start: 0.7784 (mt) cc_final: 0.7375 (tp) REVERT: B 96 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.6770 (tt0) REVERT: B 134 LYS cc_start: 0.7813 (mttt) cc_final: 0.7557 (mttt) REVERT: B 196 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7449 (m-30) REVERT: B 292 MET cc_start: 0.8374 (tpp) cc_final: 0.7147 (ttm) REVERT: B 307 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7261 (p0) outliers start: 44 outliers final: 28 residues processed: 179 average time/residue: 1.1601 time to fit residues: 227.4262 Evaluate side-chains 175 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1398 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 334 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 59 optimal weight: 6.9990 chunk 145 optimal weight: 0.8980 chunk 75 optimal weight: 0.0970 chunk 112 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1109 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.159654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131826 restraints weight = 14916.703| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.49 r_work: 0.3414 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12619 Z= 0.173 Angle : 0.637 12.261 17102 Z= 0.328 Chirality : 0.045 0.333 1891 Planarity : 0.004 0.058 2159 Dihedral : 7.401 59.096 1819 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.17 % Allowed : 16.01 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1510 helix: 0.48 (0.21), residues: 621 sheet: -1.13 (0.33), residues: 209 loop : -1.09 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 314 HIS 0.006 0.001 HIS A 475 PHE 0.020 0.002 PHE A1198 TYR 0.033 0.002 TYR A 172 ARG 0.008 0.001 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.01359 ( 1) link_NAG-ASN : angle 5.26509 ( 3) link_BETA1-4 : bond 0.00655 ( 2) link_BETA1-4 : angle 3.66590 ( 6) hydrogen bonds : bond 0.03953 ( 517) hydrogen bonds : angle 5.01466 ( 1461) SS BOND : bond 0.00251 ( 2) SS BOND : angle 1.41671 ( 4) covalent geometry : bond 0.00401 (12613) covalent geometry : angle 0.62955 (17089) Misc. bond : bond 0.00204 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 1.210 Fit side-chains REVERT: A 189 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.6547 (tmt) REVERT: A 470 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7071 (pt0) REVERT: A 574 TYR cc_start: 0.7897 (t80) cc_final: 0.7557 (t80) REVERT: A 603 TRP cc_start: 0.7654 (m100) cc_final: 0.7239 (m-10) REVERT: A 674 GLN cc_start: 0.8401 (tt0) cc_final: 0.8135 (tt0) REVERT: A 768 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6942 (mt-10) REVERT: A 792 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7679 (pp) REVERT: A 835 GLU cc_start: 0.7407 (tt0) cc_final: 0.7064 (mt-10) REVERT: A 847 LYS cc_start: 0.7699 (mttp) cc_final: 0.7454 (mtpm) REVERT: A 898 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7121 (mm) REVERT: A 916 ARG cc_start: 0.6707 (ptm-80) cc_final: 0.6396 (mtm180) REVERT: A 973 ASP cc_start: 0.7912 (m-30) cc_final: 0.7651 (m-30) REVERT: A 1036 LEU cc_start: 0.5462 (pt) cc_final: 0.5152 (pp) REVERT: A 1151 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: A 1409 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7121 (tp30) REVERT: B 54 LYS cc_start: 0.8049 (ttpt) cc_final: 0.7354 (tptt) REVERT: B 80 LEU cc_start: 0.7788 (mt) cc_final: 0.7383 (tp) REVERT: B 96 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.6772 (tt0) REVERT: B 134 LYS cc_start: 0.7823 (mttt) cc_final: 0.7561 (mttt) REVERT: B 196 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7428 (m-30) REVERT: B 292 MET cc_start: 0.8382 (tpp) cc_final: 0.7161 (ttm) REVERT: B 307 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7277 (p0) REVERT: B 388 MET cc_start: 0.6824 (mmp) cc_final: 0.6341 (mmt) outliers start: 42 outliers final: 27 residues processed: 172 average time/residue: 1.2565 time to fit residues: 235.9527 Evaluate side-chains 178 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 466 LYS Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1073 ASP Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1151 GLU Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1398 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 403 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 132 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 138 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1109 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.159402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.131173 restraints weight = 14971.153| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.54 r_work: 0.3410 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12619 Z= 0.178 Angle : 0.644 12.517 17102 Z= 0.331 Chirality : 0.045 0.320 1891 Planarity : 0.004 0.055 2159 Dihedral : 7.436 59.909 1819 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.32 % Allowed : 16.31 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1510 helix: 0.47 (0.21), residues: 625 sheet: -1.10 (0.33), residues: 209 loop : -1.11 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 314 HIS 0.006 0.001 HIS A 475 PHE 0.021 0.002 PHE A1198 TYR 0.034 0.002 TYR A 172 ARG 0.008 0.001 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.01385 ( 1) link_NAG-ASN : angle 5.23054 ( 3) link_BETA1-4 : bond 0.00652 ( 2) link_BETA1-4 : angle 3.67719 ( 6) hydrogen bonds : bond 0.03986 ( 517) hydrogen bonds : angle 5.02515 ( 1461) SS BOND : bond 0.00276 ( 2) SS BOND : angle 1.44638 ( 4) covalent geometry : bond 0.00415 (12613) covalent geometry : angle 0.63623 (17089) Misc. bond : bond 0.00202 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10593.04 seconds wall clock time: 183 minutes 12.26 seconds (10992.26 seconds total)