Starting phenix.real_space_refine on Sat Aug 23 04:27:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jw4_36679/08_2025/8jw4_36679_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jw4_36679/08_2025/8jw4_36679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jw4_36679/08_2025/8jw4_36679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jw4_36679/08_2025/8jw4_36679.map" model { file = "/net/cci-nas-00/data/ceres_data/8jw4_36679/08_2025/8jw4_36679_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jw4_36679/08_2025/8jw4_36679_neut.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 6215 2.51 5 N 1580 2.21 5 O 1747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9582 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1191, 9582 Classifications: {'peptide': 1191} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 1164} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 2.26, per 1000 atoms: 0.24 Number of scatterers: 9582 At special positions: 0 Unit cell: (72.6, 119.9, 143, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1747 8.00 N 1580 7.00 C 6215 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 351.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2260 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 62.1% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 27 through 37 removed outlier: 3.780A pdb=" N LEU A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 48 removed outlier: 3.563A pdb=" N LYS A 47 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N CYS A 48 " --> pdb=" O PRO A 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 48' Processing helix chain 'A' and resid 50 through 54 Processing helix chain 'A' and resid 55 through 63 Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.818A pdb=" N SER A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 82 " --> pdb=" O PHE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 137 removed outlier: 3.564A pdb=" N SER A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ILE A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 114 " --> pdb=" O MET A 110 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.920A pdb=" N ARG A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.796A pdb=" N PHE A 170 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 191 removed outlier: 3.553A pdb=" N LYS A 190 " --> pdb=" O TRP A 186 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 200 removed outlier: 3.527A pdb=" N CYS A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 240 removed outlier: 3.583A pdb=" N CYS A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASN A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 250 through 260 removed outlier: 4.001A pdb=" N LEU A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 305 removed outlier: 3.531A pdb=" N SER A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS A 278 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A 299 " --> pdb=" O TRP A 295 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE A 302 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 332 removed outlier: 3.542A pdb=" N LEU A 323 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 336 through 352 removed outlier: 3.501A pdb=" N ILE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 Processing helix chain 'A' and resid 449 through 454 removed outlier: 3.658A pdb=" N ARG A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 476 removed outlier: 3.700A pdb=" N ILE A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.703A pdb=" N ALA A 487 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 483 through 488' Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 530 through 539 removed outlier: 3.754A pdb=" N ASP A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 539 " --> pdb=" O VAL A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 removed outlier: 3.725A pdb=" N LEU A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 579 removed outlier: 4.634A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 607 removed outlier: 4.455A pdb=" N GLU A 598 " --> pdb=" O ASP A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 614 removed outlier: 3.573A pdb=" N ASN A 613 " --> pdb=" O GLY A 610 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG A 614 " --> pdb=" O ASN A 611 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 610 through 614' Processing helix chain 'A' and resid 685 through 694 Processing helix chain 'A' and resid 772 through 783 removed outlier: 3.994A pdb=" N ILE A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 803 removed outlier: 4.161A pdb=" N THR A 790 " --> pdb=" O LYS A 786 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE A 791 " --> pdb=" O LYS A 787 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 816 removed outlier: 3.920A pdb=" N ARG A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 849 removed outlier: 3.909A pdb=" N ASN A 826 " --> pdb=" O ASN A 822 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE A 832 " --> pdb=" O ASN A 828 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR A 833 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE A 834 " --> pdb=" O TYR A 830 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 843 " --> pdb=" O ILE A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 873 removed outlier: 3.976A pdb=" N LYS A 858 " --> pdb=" O LYS A 854 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 859 " --> pdb=" O ILE A 855 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 860 " --> pdb=" O GLY A 856 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG A 865 " --> pdb=" O LYS A 861 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG A 866 " --> pdb=" O THR A 862 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR A 873 " --> pdb=" O GLU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 927 removed outlier: 3.513A pdb=" N ALA A 891 " --> pdb=" O GLY A 887 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 893 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASN A 894 " --> pdb=" O SER A 890 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL A 897 " --> pdb=" O ILE A 893 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 904 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL A 905 " --> pdb=" O LYS A 901 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VAL A 909 " --> pdb=" O VAL A 905 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 920 " --> pdb=" O MET A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 945 removed outlier: 3.927A pdb=" N ALA A 933 " --> pdb=" O CYS A 929 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 934 " --> pdb=" O PRO A 930 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 963 removed outlier: 3.568A pdb=" N ARG A 952 " --> pdb=" O ALA A 948 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 959 " --> pdb=" O LYS A 955 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 986 removed outlier: 3.938A pdb=" N ILE A 986 " --> pdb=" O PRO A 982 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 982 through 986' Processing helix chain 'A' and resid 986 through 991 removed outlier: 3.694A pdb=" N TYR A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 999 removed outlier: 3.871A pdb=" N VAL A 996 " --> pdb=" O ASN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1006 removed outlier: 3.530A pdb=" N PHE A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1028 removed outlier: 4.177A pdb=" N TYR A1015 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS A1018 " --> pdb=" O ASP A1014 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY A1019 " --> pdb=" O TYR A1015 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ARG A1022 " --> pdb=" O LYS A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1036 removed outlier: 3.604A pdb=" N PHE A1033 " --> pdb=" O ALA A1029 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N SER A1034 " --> pdb=" O LEU A1030 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN A1035 " --> pdb=" O TRP A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1054 removed outlier: 3.714A pdb=" N LYS A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1081 removed outlier: 4.282A pdb=" N PHE A1063 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A1068 " --> pdb=" O MET A1064 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR A1069 " --> pdb=" O LYS A1065 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE A1070 " --> pdb=" O SER A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1098 removed outlier: 3.559A pdb=" N LYS A1091 " --> pdb=" O SER A1087 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A1094 " --> pdb=" O ALA A1090 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU A1095 " --> pdb=" O LYS A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1102 removed outlier: 3.584A pdb=" N ILE A1102 " --> pdb=" O PRO A1099 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1099 through 1102' Processing helix chain 'A' and resid 1169 through 1175 Processing helix chain 'A' and resid 1246 through 1250 removed outlier: 3.902A pdb=" N LEU A1250 " --> pdb=" O LEU A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1270 removed outlier: 3.847A pdb=" N ILE A1269 " --> pdb=" O ILE A1265 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A1270 " --> pdb=" O TYR A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1289 removed outlier: 3.504A pdb=" N PHE A1287 " --> pdb=" O ARG A1283 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A1288 " --> pdb=" O VAL A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1297 removed outlier: 3.942A pdb=" N LEU A1297 " --> pdb=" O ILE A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1303 removed outlier: 4.005A pdb=" N THR A1303 " --> pdb=" O LYS A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1310 Processing helix chain 'A' and resid 1313 through 1327 removed outlier: 3.605A pdb=" N GLN A1318 " --> pdb=" O GLY A1314 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG A1319 " --> pdb=" O GLY A1315 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A1327 " --> pdb=" O ALA A1323 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1358 Processing helix chain 'A' and resid 1371 through 1376 Processing helix chain 'A' and resid 1410 through 1417 Processing sheet with id=AA1, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 460 removed outlier: 6.351A pdb=" N GLY A 458 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP A 587 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 460 " --> pdb=" O ASP A 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 634 through 636 removed outlier: 5.993A pdb=" N SER A 636 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE A 670 " --> pdb=" O SER A 636 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1144 through 1145 removed outlier: 3.984A pdb=" N TYR A1144 " --> pdb=" O PHE A1133 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A1133 " --> pdb=" O TYR A1144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1144 through 1145 removed outlier: 3.984A pdb=" N TYR A1144 " --> pdb=" O PHE A1133 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A1133 " --> pdb=" O TYR A1144 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS A1129 " --> pdb=" O GLU A1231 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU A1231 " --> pdb=" O LYS A1129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1332 through 1334 removed outlier: 7.059A pdb=" N ILE A1381 " --> pdb=" O HIS A1397 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N HIS A1397 " --> pdb=" O ILE A1381 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL A1383 " --> pdb=" O GLN A1395 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A1395 " --> pdb=" O VAL A1383 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN A1385 " --> pdb=" O PHE A1393 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A1393 " --> pdb=" O ASN A1385 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2977 1.34 - 1.46: 2039 1.46 - 1.58: 4676 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 9759 Sorted by residual: bond pdb=" C TYR A 803 " pdb=" N PRO A 804 " ideal model delta sigma weight residual 1.335 1.361 -0.027 1.28e-02 6.10e+03 4.41e+00 bond pdb=" C SER A 455 " pdb=" N LYS A 456 " ideal model delta sigma weight residual 1.330 1.356 -0.026 1.36e-02 5.41e+03 3.66e+00 bond pdb=" C SER A 547 " pdb=" N LEU A 548 " ideal model delta sigma weight residual 1.327 1.358 -0.031 1.71e-02 3.42e+03 3.38e+00 bond pdb=" C LYS A 360 " pdb=" N PRO A 361 " ideal model delta sigma weight residual 1.336 1.354 -0.018 9.80e-03 1.04e+04 3.29e+00 bond pdb=" CA ASP A1275 " pdb=" CB ASP A1275 " ideal model delta sigma weight residual 1.525 1.548 -0.024 1.47e-02 4.63e+03 2.61e+00 ... (remaining 9754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 12799 1.91 - 3.82: 302 3.82 - 5.73: 41 5.73 - 7.64: 6 7.64 - 9.56: 3 Bond angle restraints: 13151 Sorted by residual: angle pdb=" C SER A1105 " pdb=" N ASN A1106 " pdb=" CA ASN A1106 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 angle pdb=" C HIS A 892 " pdb=" N ILE A 893 " pdb=" CA ILE A 893 " ideal model delta sigma weight residual 120.53 125.77 -5.24 1.41e+00 5.03e-01 1.38e+01 angle pdb=" CA ASN A1106 " pdb=" CB ASN A1106 " pdb=" CG ASN A1106 " ideal model delta sigma weight residual 112.60 115.85 -3.25 1.00e+00 1.00e+00 1.06e+01 angle pdb=" C ALA A 821 " pdb=" N ASN A 822 " pdb=" CA ASN A 822 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.47e+00 angle pdb=" N ASN A1007 " pdb=" CA ASN A1007 " pdb=" C ASN A1007 " ideal model delta sigma weight residual 114.56 111.03 3.53 1.27e+00 6.20e-01 7.74e+00 ... (remaining 13146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.35: 5580 15.35 - 30.70: 268 30.70 - 46.05: 40 46.05 - 61.40: 3 61.40 - 76.75: 3 Dihedral angle restraints: 5894 sinusoidal: 2393 harmonic: 3501 Sorted by residual: dihedral pdb=" CA LYS A1016 " pdb=" C LYS A1016 " pdb=" N ASN A1017 " pdb=" CA ASN A1017 " ideal model delta harmonic sigma weight residual -180.00 -154.41 -25.59 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA ASN A1243 " pdb=" C ASN A1243 " pdb=" N LEU A1244 " pdb=" CA LEU A1244 " ideal model delta harmonic sigma weight residual -180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA VAL A 905 " pdb=" C VAL A 905 " pdb=" N ASN A 906 " pdb=" CA ASN A 906 " ideal model delta harmonic sigma weight residual 180.00 157.00 23.00 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 5891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1232 0.055 - 0.110: 242 0.110 - 0.165: 34 0.165 - 0.220: 2 0.220 - 0.275: 1 Chirality restraints: 1511 Sorted by residual: chirality pdb=" CA ASP A 441 " pdb=" N ASP A 441 " pdb=" C ASP A 441 " pdb=" CB ASP A 441 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CB ILE A 437 " pdb=" CA ILE A 437 " pdb=" CG1 ILE A 437 " pdb=" CG2 ILE A 437 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.35e-01 chirality pdb=" CA ASN A 440 " pdb=" N ASN A 440 " pdb=" C ASN A 440 " pdb=" CB ASN A 440 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.26e-01 ... (remaining 1508 not shown) Planarity restraints: 1635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A1016 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.52e+00 pdb=" C LYS A1016 " -0.037 2.00e-02 2.50e+03 pdb=" O LYS A1016 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN A1017 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 71 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO A 72 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1257 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO A1258 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A1258 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1258 " 0.026 5.00e-02 4.00e+02 ... (remaining 1632 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1112 2.75 - 3.29: 9782 3.29 - 3.83: 13818 3.83 - 4.36: 16632 4.36 - 4.90: 28644 Nonbonded interactions: 69988 Sorted by model distance: nonbonded pdb=" OH TYR A 396 " pdb=" O GLY A 418 " model vdw 2.214 3.040 nonbonded pdb=" OD2 ASP A 144 " pdb=" OH TYR A 430 " model vdw 2.225 3.040 nonbonded pdb=" O ASN A 637 " pdb=" N ASN A 665 " model vdw 2.248 3.120 nonbonded pdb=" O ARG A 384 " pdb=" OG1 THR A 433 " model vdw 2.271 3.040 nonbonded pdb=" O LYS A 220 " pdb=" OG SER A 223 " model vdw 2.304 3.040 ... (remaining 69983 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.540 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 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 : 0.005 0.045 9759 Z= 0.226 Angle : 0.755 9.556 13151 Z= 0.420 Chirality : 0.045 0.275 1511 Planarity : 0.004 0.049 1635 Dihedral : 9.531 76.754 3634 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.28 % Allowed : 2.14 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.11 (0.20), residues: 1177 helix: -2.16 (0.17), residues: 689 sheet: -4.02 (0.45), residues: 58 loop : -3.30 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 575 TYR 0.021 0.002 TYR A 290 PHE 0.027 0.002 PHE A 294 TRP 0.016 0.002 TRP A1047 HIS 0.007 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 9759) covalent geometry : angle 0.75521 (13151) hydrogen bonds : bond 0.19593 ( 411) hydrogen bonds : angle 6.41524 ( 1188) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 223 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7464 (m-80) cc_final: 0.7195 (m-80) REVERT: A 381 LYS cc_start: 0.8325 (ttmt) cc_final: 0.8056 (ttpp) REVERT: A 382 ASN cc_start: 0.8129 (m110) cc_final: 0.7634 (p0) REVERT: A 404 LYS cc_start: 0.8512 (mtpt) cc_final: 0.8111 (ptpt) REVERT: A 463 ASP cc_start: 0.8328 (p0) cc_final: 0.7525 (t0) REVERT: A 475 ILE cc_start: 0.7953 (mt) cc_final: 0.7446 (mm) REVERT: A 520 MET cc_start: 0.5059 (mtm) cc_final: 0.4814 (ptm) REVERT: A 524 TYR cc_start: 0.7599 (m-10) cc_final: 0.7247 (m-80) REVERT: A 588 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7655 (tp30) REVERT: A 987 GLN cc_start: 0.8089 (tt0) cc_final: 0.7250 (tm-30) REVERT: A 1101 MET cc_start: 0.7749 (ptp) cc_final: 0.7525 (ptp) REVERT: A 1308 TYR cc_start: 0.7914 (m-80) cc_final: 0.7609 (m-80) REVERT: A 1336 ASP cc_start: 0.6170 (t0) cc_final: 0.5444 (t0) outliers start: 3 outliers final: 0 residues processed: 226 average time/residue: 0.0961 time to fit residues: 29.2663 Evaluate side-chains 112 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0670 chunk 117 optimal weight: 10.0000 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 443 HIS A 580 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.182886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.134469 restraints weight = 12870.717| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 3.25 r_work: 0.3705 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9759 Z= 0.135 Angle : 0.623 9.033 13151 Z= 0.327 Chirality : 0.045 0.178 1511 Planarity : 0.004 0.043 1635 Dihedral : 5.137 22.725 1287 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.03 % Allowed : 8.20 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.94 (0.23), residues: 1177 helix: -1.17 (0.19), residues: 708 sheet: -3.58 (0.49), residues: 64 loop : -2.90 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1389 TYR 0.019 0.001 TYR A1097 PHE 0.015 0.001 PHE A 43 TRP 0.013 0.001 TRP A1047 HIS 0.008 0.001 HIS A 892 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9759) covalent geometry : angle 0.62324 (13151) hydrogen bonds : bond 0.05944 ( 411) hydrogen bonds : angle 4.55997 ( 1188) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7583 (m-80) cc_final: 0.7332 (m-80) REVERT: A 89 ASP cc_start: 0.6095 (OUTLIER) cc_final: 0.5839 (p0) REVERT: A 275 GLU cc_start: 0.7212 (mt-10) cc_final: 0.7001 (mt-10) REVERT: A 375 ILE cc_start: 0.3954 (mt) cc_final: 0.3634 (mp) REVERT: A 379 GLU cc_start: 0.6441 (tm-30) cc_final: 0.6164 (tm-30) REVERT: A 381 LYS cc_start: 0.8067 (ttmt) cc_final: 0.7834 (ttpp) REVERT: A 382 ASN cc_start: 0.8338 (m110) cc_final: 0.7654 (p0) REVERT: A 404 LYS cc_start: 0.8240 (mtpt) cc_final: 0.7849 (ptpt) REVERT: A 434 GLU cc_start: 0.6065 (mt-10) cc_final: 0.5791 (mm-30) REVERT: A 456 LYS cc_start: 0.4656 (mmtp) cc_final: 0.3606 (pttm) REVERT: A 463 ASP cc_start: 0.8159 (p0) cc_final: 0.7403 (t0) REVERT: A 520 MET cc_start: 0.4965 (mtm) cc_final: 0.4721 (ptm) REVERT: A 524 TYR cc_start: 0.7210 (m-10) cc_final: 0.6935 (m-10) REVERT: A 588 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7663 (tp30) REVERT: A 622 ARG cc_start: 0.8203 (ttp-110) cc_final: 0.7849 (tpp-160) REVERT: A 916 MET cc_start: 0.8030 (tpt) cc_final: 0.7778 (tpt) REVERT: A 987 GLN cc_start: 0.8407 (tt0) cc_final: 0.7778 (tm-30) outliers start: 11 outliers final: 4 residues processed: 132 average time/residue: 0.0950 time to fit residues: 17.5953 Evaluate side-chains 105 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1148 SER Chi-restraints excluded: chain A residue 1150 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 79 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 49 optimal weight: 0.0370 chunk 31 optimal weight: 0.8980 chunk 108 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 191 ASN A 826 ASN ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.178926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.129229 restraints weight = 13039.990| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.20 r_work: 0.3640 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9759 Z= 0.131 Angle : 0.578 9.278 13151 Z= 0.304 Chirality : 0.044 0.160 1511 Planarity : 0.004 0.041 1635 Dihedral : 4.832 22.907 1287 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.12 % Allowed : 9.60 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.23), residues: 1177 helix: -0.67 (0.19), residues: 706 sheet: -3.14 (0.54), residues: 64 loop : -2.73 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1371 TYR 0.018 0.001 TYR A1097 PHE 0.013 0.001 PHE A 43 TRP 0.011 0.001 TRP A1047 HIS 0.004 0.001 HIS A 892 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9759) covalent geometry : angle 0.57821 (13151) hydrogen bonds : bond 0.05403 ( 411) hydrogen bonds : angle 4.18705 ( 1188) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7355 (m-80) cc_final: 0.6614 (m-80) REVERT: A 275 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6886 (mt-10) REVERT: A 375 ILE cc_start: 0.3968 (mt) cc_final: 0.3762 (mp) REVERT: A 379 GLU cc_start: 0.6668 (tm-30) cc_final: 0.5777 (tm-30) REVERT: A 382 ASN cc_start: 0.8305 (m110) cc_final: 0.7638 (p0) REVERT: A 404 LYS cc_start: 0.8147 (mtpt) cc_final: 0.7840 (ptpt) REVERT: A 434 GLU cc_start: 0.6119 (mt-10) cc_final: 0.5839 (mm-30) REVERT: A 456 LYS cc_start: 0.4733 (mmtp) cc_final: 0.3601 (pttm) REVERT: A 463 ASP cc_start: 0.8289 (p0) cc_final: 0.7596 (t0) REVERT: A 524 TYR cc_start: 0.7109 (m-10) cc_final: 0.6694 (m-80) REVERT: A 588 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7296 (tm-30) REVERT: A 622 ARG cc_start: 0.8124 (ttp-110) cc_final: 0.7867 (tpp-160) REVERT: A 776 ARG cc_start: 0.8172 (ptt90) cc_final: 0.7585 (ptt-90) REVERT: A 916 MET cc_start: 0.8109 (tpt) cc_final: 0.7897 (tpt) REVERT: A 987 GLN cc_start: 0.8703 (tt0) cc_final: 0.8010 (tm-30) REVERT: A 1011 LYS cc_start: 0.5845 (mmmt) cc_final: 0.5619 (tppt) REVERT: A 1356 ASP cc_start: 0.9096 (t70) cc_final: 0.8894 (m-30) outliers start: 12 outliers final: 6 residues processed: 126 average time/residue: 0.0887 time to fit residues: 15.8213 Evaluate side-chains 104 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1148 SER Chi-restraints excluded: chain A residue 1150 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 34 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 0.0270 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.1040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1256 GLN A1262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.174405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.123943 restraints weight = 13254.555| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.21 r_work: 0.3574 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9759 Z= 0.140 Angle : 0.571 9.284 13151 Z= 0.302 Chirality : 0.044 0.152 1511 Planarity : 0.004 0.042 1635 Dihedral : 4.750 22.294 1287 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.40 % Allowed : 11.93 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.24), residues: 1177 helix: -0.52 (0.20), residues: 717 sheet: -2.31 (0.61), residues: 59 loop : -2.71 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1389 TYR 0.018 0.001 TYR A1097 PHE 0.023 0.001 PHE A1293 TRP 0.011 0.001 TRP A1047 HIS 0.003 0.001 HIS A 892 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9759) covalent geometry : angle 0.57095 (13151) hydrogen bonds : bond 0.05407 ( 411) hydrogen bonds : angle 4.06264 ( 1188) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7322 (m-80) cc_final: 0.6422 (m-80) REVERT: A 226 TYR cc_start: 0.8190 (m-10) cc_final: 0.7907 (m-80) REVERT: A 382 ASN cc_start: 0.8316 (m110) cc_final: 0.7616 (p0) REVERT: A 404 LYS cc_start: 0.8317 (mtpt) cc_final: 0.7948 (ptpt) REVERT: A 463 ASP cc_start: 0.8323 (p0) cc_final: 0.7590 (t0) REVERT: A 524 TYR cc_start: 0.7173 (m-10) cc_final: 0.6739 (m-80) REVERT: A 588 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7635 (tp30) REVERT: A 776 ARG cc_start: 0.8233 (ptt90) cc_final: 0.7726 (ptt-90) REVERT: A 987 GLN cc_start: 0.8683 (tt0) cc_final: 0.8194 (tm-30) REVERT: A 1287 PHE cc_start: 0.7697 (m-10) cc_final: 0.7482 (m-10) REVERT: A 1356 ASP cc_start: 0.9130 (t70) cc_final: 0.8905 (m-30) outliers start: 15 outliers final: 9 residues processed: 116 average time/residue: 0.0916 time to fit residues: 15.0593 Evaluate side-chains 99 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1148 SER Chi-restraints excluded: chain A residue 1150 THR Chi-restraints excluded: chain A residue 1367 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 37 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.173878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.123350 restraints weight = 13244.332| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.21 r_work: 0.3563 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9759 Z= 0.129 Angle : 0.554 9.743 13151 Z= 0.294 Chirality : 0.043 0.155 1511 Planarity : 0.003 0.043 1635 Dihedral : 4.641 21.785 1287 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.49 % Allowed : 13.05 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.24), residues: 1177 helix: -0.33 (0.20), residues: 719 sheet: -1.88 (0.66), residues: 59 loop : -2.61 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1371 TYR 0.017 0.001 TYR A1097 PHE 0.024 0.001 PHE A1293 TRP 0.009 0.001 TRP A1047 HIS 0.003 0.001 HIS A 443 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9759) covalent geometry : angle 0.55361 (13151) hydrogen bonds : bond 0.05178 ( 411) hydrogen bonds : angle 3.97270 ( 1188) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7270 (m-80) cc_final: 0.6371 (m-80) REVERT: A 226 TYR cc_start: 0.8213 (m-80) cc_final: 0.7893 (m-80) REVERT: A 256 LYS cc_start: 0.7249 (mmtt) cc_final: 0.6957 (mtpt) REVERT: A 382 ASN cc_start: 0.8228 (m110) cc_final: 0.7499 (p0) REVERT: A 404 LYS cc_start: 0.8266 (mtpt) cc_final: 0.7831 (ptpt) REVERT: A 463 ASP cc_start: 0.8352 (p0) cc_final: 0.7626 (t0) REVERT: A 524 TYR cc_start: 0.7152 (m-10) cc_final: 0.6731 (m-80) REVERT: A 588 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7424 (tp30) REVERT: A 776 ARG cc_start: 0.8315 (ptt90) cc_final: 0.7768 (ptt-90) REVERT: A 987 GLN cc_start: 0.8758 (tt0) cc_final: 0.8313 (tm-30) REVERT: A 988 GLU cc_start: 0.7780 (tt0) cc_final: 0.7403 (tp30) outliers start: 16 outliers final: 11 residues processed: 112 average time/residue: 0.0876 time to fit residues: 13.9284 Evaluate side-chains 106 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1148 SER Chi-restraints excluded: chain A residue 1150 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 116 optimal weight: 9.9990 chunk 69 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.174751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.124743 restraints weight = 13115.778| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 3.18 r_work: 0.3582 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9759 Z= 0.112 Angle : 0.537 10.939 13151 Z= 0.281 Chirality : 0.042 0.140 1511 Planarity : 0.003 0.044 1635 Dihedral : 4.505 21.177 1287 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.96 % Allowed : 12.77 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.24), residues: 1177 helix: -0.11 (0.20), residues: 716 sheet: -1.59 (0.68), residues: 59 loop : -2.55 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 384 TYR 0.015 0.001 TYR A1097 PHE 0.028 0.001 PHE A1293 TRP 0.009 0.001 TRP A1047 HIS 0.003 0.001 HIS A 443 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9759) covalent geometry : angle 0.53725 (13151) hydrogen bonds : bond 0.04749 ( 411) hydrogen bonds : angle 3.84829 ( 1188) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7182 (m-80) cc_final: 0.6334 (m-80) REVERT: A 133 ARG cc_start: 0.6775 (tmm160) cc_final: 0.6321 (tmm160) REVERT: A 152 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6808 (ptm160) REVERT: A 226 TYR cc_start: 0.8144 (m-80) cc_final: 0.7815 (m-80) REVERT: A 256 LYS cc_start: 0.7201 (mmtt) cc_final: 0.6923 (mtpt) REVERT: A 382 ASN cc_start: 0.8167 (m110) cc_final: 0.7439 (p0) REVERT: A 404 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7827 (ptpt) REVERT: A 524 TYR cc_start: 0.7214 (m-10) cc_final: 0.6768 (m-80) REVERT: A 588 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7514 (tp30) REVERT: A 776 ARG cc_start: 0.8275 (ptt90) cc_final: 0.7714 (ptt-90) REVERT: A 987 GLN cc_start: 0.8751 (tt0) cc_final: 0.8445 (tm-30) REVERT: A 988 GLU cc_start: 0.7824 (tt0) cc_final: 0.7541 (tp30) REVERT: A 1092 LEU cc_start: 0.7932 (mt) cc_final: 0.7674 (pp) REVERT: A 1349 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8179 (tp) REVERT: A 1356 ASP cc_start: 0.9144 (t70) cc_final: 0.8903 (m-30) outliers start: 21 outliers final: 11 residues processed: 119 average time/residue: 0.0957 time to fit residues: 16.0543 Evaluate side-chains 109 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1148 SER Chi-restraints excluded: chain A residue 1150 THR Chi-restraints excluded: chain A residue 1344 SER Chi-restraints excluded: chain A residue 1349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 4 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 81 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 56 optimal weight: 0.0470 chunk 73 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 overall best weight: 0.4880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.175829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.125780 restraints weight = 13139.702| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 3.24 r_work: 0.3595 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9759 Z= 0.104 Angle : 0.525 11.237 13151 Z= 0.272 Chirality : 0.042 0.168 1511 Planarity : 0.003 0.044 1635 Dihedral : 4.365 20.639 1287 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.86 % Allowed : 13.70 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.24), residues: 1177 helix: 0.05 (0.20), residues: 716 sheet: -1.40 (0.69), residues: 59 loop : -2.46 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 384 TYR 0.013 0.001 TYR A1097 PHE 0.028 0.001 PHE A1293 TRP 0.008 0.001 TRP A1047 HIS 0.003 0.001 HIS A1400 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 9759) covalent geometry : angle 0.52550 (13151) hydrogen bonds : bond 0.04327 ( 411) hydrogen bonds : angle 3.71516 ( 1188) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7140 (m-80) cc_final: 0.6282 (m-80) REVERT: A 133 ARG cc_start: 0.6773 (tmm160) cc_final: 0.6341 (tmm160) REVERT: A 152 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6763 (ptm160) REVERT: A 256 LYS cc_start: 0.7111 (mmtt) cc_final: 0.6870 (mtpt) REVERT: A 382 ASN cc_start: 0.8230 (m110) cc_final: 0.7468 (p0) REVERT: A 404 LYS cc_start: 0.8287 (mtpt) cc_final: 0.7801 (ptpt) REVERT: A 434 GLU cc_start: 0.5790 (OUTLIER) cc_final: 0.4901 (mm-30) REVERT: A 463 ASP cc_start: 0.8533 (p0) cc_final: 0.7468 (t0) REVERT: A 524 TYR cc_start: 0.7256 (m-10) cc_final: 0.6824 (m-80) REVERT: A 588 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7452 (tp30) REVERT: A 776 ARG cc_start: 0.8244 (ptt90) cc_final: 0.7683 (ptt-90) REVERT: A 987 GLN cc_start: 0.8709 (tt0) cc_final: 0.8425 (tm-30) REVERT: A 988 GLU cc_start: 0.7764 (tt0) cc_final: 0.7538 (tp30) REVERT: A 1092 LEU cc_start: 0.7952 (mt) cc_final: 0.7681 (pp) REVERT: A 1118 ASN cc_start: 0.7218 (p0) cc_final: 0.7001 (p0) REVERT: A 1259 MET cc_start: 0.8175 (tpt) cc_final: 0.7883 (tpt) REVERT: A 1356 ASP cc_start: 0.9141 (t70) cc_final: 0.8847 (m-30) outliers start: 20 outliers final: 13 residues processed: 116 average time/residue: 0.0964 time to fit residues: 15.7700 Evaluate side-chains 112 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1148 SER Chi-restraints excluded: chain A residue 1150 THR Chi-restraints excluded: chain A residue 1336 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 104 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 84 optimal weight: 0.0060 chunk 96 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 1 optimal weight: 0.1980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.175403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.125117 restraints weight = 13152.659| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.24 r_work: 0.3583 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9759 Z= 0.108 Angle : 0.540 10.961 13151 Z= 0.278 Chirality : 0.042 0.169 1511 Planarity : 0.003 0.044 1635 Dihedral : 4.312 20.384 1287 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.77 % Allowed : 14.17 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.24), residues: 1177 helix: 0.16 (0.20), residues: 710 sheet: -1.12 (0.71), residues: 58 loop : -2.50 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 384 TYR 0.013 0.001 TYR A1097 PHE 0.028 0.001 PHE A1293 TRP 0.007 0.001 TRP A1047 HIS 0.003 0.001 HIS A 443 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 9759) covalent geometry : angle 0.54033 (13151) hydrogen bonds : bond 0.04377 ( 411) hydrogen bonds : angle 3.67832 ( 1188) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7158 (m-80) cc_final: 0.6286 (m-80) REVERT: A 133 ARG cc_start: 0.6774 (tmm160) cc_final: 0.6373 (tmm160) REVERT: A 152 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6776 (ptm160) REVERT: A 256 LYS cc_start: 0.7205 (mmtt) cc_final: 0.6929 (mtpt) REVERT: A 382 ASN cc_start: 0.8233 (m110) cc_final: 0.7480 (p0) REVERT: A 404 LYS cc_start: 0.8320 (mtpt) cc_final: 0.7816 (ptpt) REVERT: A 434 GLU cc_start: 0.5808 (OUTLIER) cc_final: 0.4920 (mm-30) REVERT: A 524 TYR cc_start: 0.7266 (m-10) cc_final: 0.6841 (m-80) REVERT: A 588 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7338 (tm-30) REVERT: A 987 GLN cc_start: 0.8620 (tt0) cc_final: 0.8345 (tm-30) REVERT: A 988 GLU cc_start: 0.7812 (tt0) cc_final: 0.7596 (tp30) REVERT: A 993 MET cc_start: 0.7745 (tpp) cc_final: 0.7414 (mmm) REVERT: A 1092 LEU cc_start: 0.7967 (mt) cc_final: 0.7693 (pp) outliers start: 19 outliers final: 16 residues processed: 109 average time/residue: 0.0873 time to fit residues: 13.5315 Evaluate side-chains 110 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1148 SER Chi-restraints excluded: chain A residue 1150 THR Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1336 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 39 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.171831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.121103 restraints weight = 13215.632| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.18 r_work: 0.3542 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9759 Z= 0.142 Angle : 0.577 12.674 13151 Z= 0.300 Chirality : 0.044 0.166 1511 Planarity : 0.003 0.042 1635 Dihedral : 4.472 21.289 1287 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.96 % Allowed : 14.26 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.24), residues: 1177 helix: 0.10 (0.20), residues: 705 sheet: -1.04 (0.72), residues: 58 loop : -2.56 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 570 TYR 0.017 0.001 TYR A1097 PHE 0.027 0.001 PHE A1293 TRP 0.007 0.001 TRP A 186 HIS 0.003 0.001 HIS A 892 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9759) covalent geometry : angle 0.57734 (13151) hydrogen bonds : bond 0.05237 ( 411) hydrogen bonds : angle 3.85236 ( 1188) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7210 (m-80) cc_final: 0.6336 (m-80) REVERT: A 133 ARG cc_start: 0.6793 (tmm160) cc_final: 0.6356 (tmm160) REVERT: A 152 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6857 (ptm160) REVERT: A 256 LYS cc_start: 0.7321 (mmtt) cc_final: 0.7034 (mtpt) REVERT: A 382 ASN cc_start: 0.8265 (m110) cc_final: 0.7520 (p0) REVERT: A 404 LYS cc_start: 0.8273 (mtpt) cc_final: 0.7715 (ptpt) REVERT: A 407 LYS cc_start: 0.7205 (mttt) cc_final: 0.6788 (mtpt) REVERT: A 434 GLU cc_start: 0.5791 (OUTLIER) cc_final: 0.4901 (mm-30) REVERT: A 463 ASP cc_start: 0.8544 (p0) cc_final: 0.7583 (t0) REVERT: A 524 TYR cc_start: 0.7205 (m-10) cc_final: 0.6772 (m-80) REVERT: A 588 GLU cc_start: 0.8469 (mt-10) cc_final: 0.7498 (tm-30) REVERT: A 987 GLN cc_start: 0.8779 (tt0) cc_final: 0.8485 (tm-30) REVERT: A 1092 LEU cc_start: 0.8016 (mt) cc_final: 0.7729 (pp) REVERT: A 1349 LEU cc_start: 0.8443 (tp) cc_final: 0.8194 (tp) outliers start: 21 outliers final: 16 residues processed: 112 average time/residue: 0.0969 time to fit residues: 15.3721 Evaluate side-chains 112 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1148 SER Chi-restraints excluded: chain A residue 1150 THR Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1336 ASP Chi-restraints excluded: chain A residue 1367 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 96 optimal weight: 0.4980 chunk 114 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.172068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.121479 restraints weight = 13225.606| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 3.18 r_work: 0.3549 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9759 Z= 0.131 Angle : 0.574 12.958 13151 Z= 0.296 Chirality : 0.043 0.163 1511 Planarity : 0.003 0.043 1635 Dihedral : 4.459 22.607 1287 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.58 % Allowed : 14.63 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.24), residues: 1177 helix: 0.13 (0.20), residues: 708 sheet: -0.92 (0.72), residues: 58 loop : -2.47 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 622 TYR 0.015 0.001 TYR A1097 PHE 0.029 0.001 PHE A1293 TRP 0.008 0.001 TRP A 186 HIS 0.003 0.001 HIS A 892 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9759) covalent geometry : angle 0.57369 (13151) hydrogen bonds : bond 0.05010 ( 411) hydrogen bonds : angle 3.81140 ( 1188) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7197 (m-80) cc_final: 0.6330 (m-80) REVERT: A 133 ARG cc_start: 0.6776 (tmm160) cc_final: 0.6345 (tmm160) REVERT: A 152 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6862 (ptm160) REVERT: A 256 LYS cc_start: 0.7284 (mmtt) cc_final: 0.7010 (mtpt) REVERT: A 382 ASN cc_start: 0.8281 (m110) cc_final: 0.7542 (p0) REVERT: A 404 LYS cc_start: 0.8255 (mtpt) cc_final: 0.7724 (pttm) REVERT: A 407 LYS cc_start: 0.7380 (mttt) cc_final: 0.7026 (mtpt) REVERT: A 434 GLU cc_start: 0.5811 (OUTLIER) cc_final: 0.4969 (mm-30) REVERT: A 463 ASP cc_start: 0.8552 (p0) cc_final: 0.7576 (t0) REVERT: A 524 TYR cc_start: 0.7288 (m-10) cc_final: 0.6872 (m-80) REVERT: A 588 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7518 (tm-30) REVERT: A 987 GLN cc_start: 0.8839 (tt0) cc_final: 0.8588 (tm-30) REVERT: A 1092 LEU cc_start: 0.8011 (mt) cc_final: 0.7720 (pp) REVERT: A 1259 MET cc_start: 0.8351 (tpt) cc_final: 0.7764 (tpt) REVERT: A 1349 LEU cc_start: 0.8445 (tp) cc_final: 0.8196 (tp) outliers start: 17 outliers final: 13 residues processed: 107 average time/residue: 0.0922 time to fit residues: 13.9856 Evaluate side-chains 103 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1148 SER Chi-restraints excluded: chain A residue 1150 THR Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1336 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 90 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 107 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.172401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.122012 restraints weight = 13137.331| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 3.17 r_work: 0.3554 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9759 Z= 0.125 Angle : 0.578 12.886 13151 Z= 0.296 Chirality : 0.043 0.180 1511 Planarity : 0.003 0.043 1635 Dihedral : 4.417 22.403 1287 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.58 % Allowed : 15.00 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.24), residues: 1177 helix: 0.18 (0.20), residues: 705 sheet: -0.36 (0.81), residues: 48 loop : -2.48 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 384 TYR 0.014 0.001 TYR A1097 PHE 0.029 0.001 PHE A1293 TRP 0.008 0.001 TRP A 186 HIS 0.003 0.001 HIS A 892 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9759) covalent geometry : angle 0.57772 (13151) hydrogen bonds : bond 0.04868 ( 411) hydrogen bonds : angle 3.78920 ( 1188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2309.61 seconds wall clock time: 40 minutes 15.89 seconds (2415.89 seconds total)