Starting phenix.real_space_refine on Fri Feb 14 03:15:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jw4_36679/02_2025/8jw4_36679_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jw4_36679/02_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_36679/02_2025/8jw4_36679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jw4_36679/02_2025/8jw4_36679.map" model { file = "/net/cci-nas-00/data/ceres_data/8jw4_36679/02_2025/8jw4_36679_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jw4_36679/02_2025/8jw4_36679_neut.cif" } resolution = 3.13 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= -0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.05, per 1000 atoms: 0.53 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: 2.21 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.18 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: 3.16 Time building geometry restraints manager: 2.58 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: 1.100 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 22.860 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.540 ------------------------------------------------------------------------------- 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= 0.322 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 (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: -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 TRP 0.016 0.002 TRP A1047 HIS 0.007 0.001 HIS A 278 PHE 0.027 0.002 PHE A 294 TYR 0.021 0.002 TYR A 290 ARG 0.008 0.001 ARG A 575 *********************** 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 : 1.124 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: 0.7464 (m-80) cc_final: 0.7195 (m-80) REVERT: A 381 LYS cc_start: 0.8325 (ttmt) cc_final: 0.8035 (ttpp) REVERT: A 382 ASN cc_start: 0.8129 (m110) cc_final: 0.7536 (p0) REVERT: A 404 LYS cc_start: 0.8512 (mtpt) cc_final: 0.8110 (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: 0.4813 (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: 0.7253 (tm-30) REVERT: A 1101 MET cc_start: 0.7749 (ptp) cc_final: 0.7525 (ptp) REVERT: A 1267 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7449 (tp30) 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: 0.5443 (t0) outliers start: 3 outliers final: 0 residues processed: 226 average time/residue: 0.2603 time to fit residues: 79.1442 Evaluate side-chains 115 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 0.0870 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- 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 = 0.4328 r_free = 0.4328 target = 0.180077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.130868 restraints weight = 12871.540| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 3.19 r_work: 0.3665 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9759 Z= 0.210 Angle : 0.638 8.994 13151 Z= 0.337 Chirality : 0.046 0.173 1511 Planarity : 0.004 0.045 1635 Dihedral : 5.213 23.165 1287 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.03 % Allowed : 8.29 % Favored : 90.68 % 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: -2.97 (0.22), residues: 1177 helix: -1.19 (0.19), residues: 708 sheet: -3.59 (0.49), residues: 64 loop : -2.93 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1047 HIS 0.019 0.002 HIS A 676 PHE 0.016 0.001 PHE A 43 TYR 0.021 0.002 TYR A1097 ARG 0.006 0.001 ARG A 384 *********************** 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 141 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7540 (m-80) cc_final: 0.7312 (m-80) REVERT: A 89 ASP cc_start: 0.6270 (OUTLIER) cc_final: 0.6006 (p0) REVERT: A 375 ILE cc_start: 0.3987 (mt) cc_final: 0.3696 (mp) REVERT: A 379 GLU cc_start: 0.6474 (tm-30) cc_final: 0.5778 (tm-30) REVERT: A 382 ASN cc_start: 0.8351 (m110) cc_final: 0.7671 (p0) REVERT: A 404 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7793 (ptpt) REVERT: A 434 GLU cc_start: 0.6084 (mt-10) cc_final: 0.5807 (mm-30) REVERT: A 456 LYS cc_start: 0.4738 (mmtp) cc_final: 0.3696 (pttm) REVERT: A 463 ASP cc_start: 0.8255 (p0) cc_final: 0.7507 (t0) REVERT: A 524 TYR cc_start: 0.7199 (m-10) cc_final: 0.6915 (m-10) REVERT: A 588 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7692 (tp30) REVERT: A 622 ARG cc_start: 0.8181 (ttp-110) cc_final: 0.7845 (tpp-160) REVERT: A 916 MET cc_start: 0.8163 (tpt) cc_final: 0.7919 (tpt) REVERT: A 987 GLN cc_start: 0.8347 (tt0) cc_final: 0.7731 (tm-30) REVERT: A 1267 GLU cc_start: 0.8579 (mm-30) cc_final: 0.7941 (tp30) REVERT: A 1356 ASP cc_start: 0.9114 (t70) cc_final: 0.8894 (m-30) outliers start: 11 outliers final: 7 residues processed: 137 average time/residue: 0.2481 time to fit residues: 47.7788 Evaluate side-chains 110 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1148 SER Chi-restraints excluded: chain A residue 1150 THR Chi-restraints excluded: chain A residue 1295 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 102 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 78 optimal weight: 0.1980 chunk 58 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 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 191 ASN A 826 ASN ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.178685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.128984 restraints weight = 13095.106| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 3.27 r_work: 0.3635 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9759 Z= 0.167 Angle : 0.572 9.437 13151 Z= 0.300 Chirality : 0.043 0.156 1511 Planarity : 0.004 0.042 1635 Dihedral : 4.862 22.610 1287 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.21 % Allowed : 10.16 % Favored : 88.63 % 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: -2.35 (0.23), residues: 1177 helix: -0.71 (0.19), residues: 708 sheet: -3.09 (0.54), residues: 64 loop : -2.70 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1047 HIS 0.004 0.001 HIS A 892 PHE 0.012 0.001 PHE A 43 TYR 0.017 0.001 TYR A1097 ARG 0.006 0.000 ARG A1371 *********************** 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 127 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7435 (m-80) cc_final: 0.6689 (m-80) REVERT: A 382 ASN cc_start: 0.8434 (m110) cc_final: 0.7785 (p0) REVERT: A 404 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7758 (ptpt) REVERT: A 434 GLU cc_start: 0.6059 (mt-10) cc_final: 0.5796 (mm-30) REVERT: A 463 ASP cc_start: 0.8287 (p0) cc_final: 0.7592 (t0) REVERT: A 524 TYR cc_start: 0.7097 (m-10) cc_final: 0.6684 (m-80) REVERT: A 588 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7772 (tp30) REVERT: A 776 ARG cc_start: 0.8161 (ptt90) cc_final: 0.7576 (ptt-90) REVERT: A 916 MET cc_start: 0.8107 (tpt) cc_final: 0.7887 (tpt) REVERT: A 987 GLN cc_start: 0.8575 (tt0) cc_final: 0.7799 (tm-30) REVERT: A 1011 LYS cc_start: 0.5776 (mmmt) cc_final: 0.5552 (tppt) REVERT: A 1256 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7478 (mm110) REVERT: A 1267 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8058 (tp30) REVERT: A 1356 ASP cc_start: 0.9098 (t70) cc_final: 0.8894 (m-30) REVERT: A 1362 ASP cc_start: 0.8070 (p0) cc_final: 0.7683 (p0) outliers start: 13 outliers final: 6 residues processed: 123 average time/residue: 0.2071 time to fit residues: 36.1933 Evaluate side-chains 101 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 861 LYS 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 71 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 54 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A1256 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.176892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.126830 restraints weight = 12902.329| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 3.23 r_work: 0.3608 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9759 Z= 0.162 Angle : 0.551 9.516 13151 Z= 0.291 Chirality : 0.043 0.150 1511 Planarity : 0.004 0.043 1635 Dihedral : 4.689 21.846 1287 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.12 % Allowed : 12.02 % Favored : 86.86 % 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: -1.93 (0.24), residues: 1177 helix: -0.37 (0.20), residues: 709 sheet: -2.56 (0.58), residues: 64 loop : -2.63 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1047 HIS 0.003 0.001 HIS A 892 PHE 0.024 0.001 PHE A1293 TYR 0.018 0.001 TYR A1097 ARG 0.004 0.000 ARG A1389 *********************** 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 122 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7344 (m-80) cc_final: 0.6463 (m-80) REVERT: A 231 MET cc_start: 0.8733 (mmp) cc_final: 0.8518 (mmp) REVERT: A 382 ASN cc_start: 0.8332 (m110) cc_final: 0.7605 (p0) REVERT: A 404 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7730 (ptpt) REVERT: A 434 GLU cc_start: 0.6168 (mt-10) cc_final: 0.5824 (mm-30) REVERT: A 463 ASP cc_start: 0.8323 (p0) cc_final: 0.7599 (t0) REVERT: A 524 TYR cc_start: 0.7154 (m-10) cc_final: 0.6733 (m-80) REVERT: A 588 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7619 (tp30) REVERT: A 776 ARG cc_start: 0.8270 (ptt90) cc_final: 0.7751 (ptt-90) REVERT: A 987 GLN cc_start: 0.8672 (tt0) cc_final: 0.8039 (tm-30) REVERT: A 1092 LEU cc_start: 0.8007 (mt) cc_final: 0.7744 (pp) REVERT: A 1267 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8149 (tp30) REVERT: A 1287 PHE cc_start: 0.7739 (m-10) cc_final: 0.7509 (m-10) REVERT: A 1356 ASP cc_start: 0.9128 (t70) cc_final: 0.8899 (m-30) outliers start: 12 outliers final: 7 residues processed: 119 average time/residue: 0.2113 time to fit residues: 35.6536 Evaluate side-chains 104 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 1080 LEU 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 69 optimal weight: 0.6980 chunk 101 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 116 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4296 r_free = 0.4296 target = 0.176275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.126019 restraints weight = 12935.963| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 3.21 r_work: 0.3600 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9759 Z= 0.155 Angle : 0.538 10.272 13151 Z= 0.282 Chirality : 0.042 0.155 1511 Planarity : 0.003 0.043 1635 Dihedral : 4.523 21.423 1287 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.77 % Allowed : 12.21 % Favored : 86.02 % 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: -1.65 (0.24), residues: 1177 helix: -0.17 (0.20), residues: 704 sheet: -2.21 (0.61), residues: 64 loop : -2.46 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1047 HIS 0.003 0.001 HIS A 443 PHE 0.021 0.001 PHE A1293 TYR 0.016 0.001 TYR A1097 ARG 0.003 0.000 ARG A1371 *********************** 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 129 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7305 (m-80) cc_final: 0.6390 (m-80) REVERT: A 160 GLU cc_start: 0.8103 (tt0) cc_final: 0.7860 (tp30) REVERT: A 226 TYR cc_start: 0.8144 (m-10) cc_final: 0.7828 (m-80) REVERT: A 375 ILE cc_start: 0.4050 (mt) cc_final: 0.3837 (mp) REVERT: A 382 ASN cc_start: 0.8257 (m110) cc_final: 0.7540 (p0) REVERT: A 404 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7728 (pttm) REVERT: A 456 LYS cc_start: 0.4994 (mmtp) cc_final: 0.3931 (pttm) REVERT: A 463 ASP cc_start: 0.8343 (p0) cc_final: 0.7626 (t0) REVERT: A 524 TYR cc_start: 0.7149 (m-10) cc_final: 0.6671 (m-80) REVERT: A 588 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7491 (tp30) REVERT: A 776 ARG cc_start: 0.8257 (ptt90) cc_final: 0.7714 (ptt-90) REVERT: A 987 GLN cc_start: 0.8689 (tt0) cc_final: 0.8152 (tm-30) REVERT: A 1267 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8195 (tp30) REVERT: A 1349 LEU cc_start: 0.8490 (tp) cc_final: 0.8244 (tp) REVERT: A 1356 ASP cc_start: 0.9110 (t70) cc_final: 0.8887 (m-30) outliers start: 19 outliers final: 12 residues processed: 123 average time/residue: 0.2208 time to fit residues: 38.5278 Evaluate side-chains 111 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 152 ARG Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 439 VAL 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 1367 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 46 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 107 optimal weight: 0.0270 overall best weight: 0.6842 ------------------------------------------------------------------------------- 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 = 0.4297 r_free = 0.4297 target = 0.176043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.125850 restraints weight = 13023.072| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 3.25 r_work: 0.3596 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.3926 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= 0.149 Angle : 0.532 10.622 13151 Z= 0.279 Chirality : 0.042 0.161 1511 Planarity : 0.003 0.044 1635 Dihedral : 4.428 21.068 1287 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.77 % Allowed : 13.89 % Favored : 84.34 % 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: -1.45 (0.24), residues: 1177 helix: -0.01 (0.20), residues: 713 sheet: -1.87 (0.64), residues: 64 loop : -2.50 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1047 HIS 0.003 0.001 HIS A1400 PHE 0.025 0.001 PHE A1293 TYR 0.015 0.001 TYR A1097 ARG 0.002 0.000 ARG A1389 *********************** 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 123 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7169 (m-80) cc_final: 0.6313 (m-80) REVERT: A 133 ARG cc_start: 0.6767 (tmm160) cc_final: 0.6305 (tmm160) REVERT: A 152 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6957 (ptm160) REVERT: A 256 LYS cc_start: 0.7191 (mmtt) cc_final: 0.6921 (mtpt) REVERT: A 382 ASN cc_start: 0.8251 (m110) cc_final: 0.7559 (p0) REVERT: A 404 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7749 (pttm) REVERT: A 434 GLU cc_start: 0.6105 (mt-10) cc_final: 0.5486 (mm-30) REVERT: A 463 ASP cc_start: 0.8340 (p0) cc_final: 0.7625 (t0) REVERT: A 524 TYR cc_start: 0.7134 (m-10) cc_final: 0.6675 (m-80) REVERT: A 588 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7488 (tp30) REVERT: A 776 ARG cc_start: 0.8276 (ptt90) cc_final: 0.7710 (ptt-90) REVERT: A 987 GLN cc_start: 0.8613 (tt0) cc_final: 0.8210 (tm-30) REVERT: A 1092 LEU cc_start: 0.7906 (mt) cc_final: 0.7650 (pp) REVERT: A 1267 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8262 (tp30) REVERT: A 1349 LEU cc_start: 0.8428 (tp) cc_final: 0.8153 (tp) REVERT: A 1356 ASP cc_start: 0.9128 (t70) cc_final: 0.8890 (m-30) outliers start: 19 outliers final: 13 residues processed: 116 average time/residue: 0.2295 time to fit residues: 37.3503 Evaluate side-chains 107 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 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 1336 ASP Chi-restraints excluded: chain A residue 1344 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 97 optimal weight: 0.0000 chunk 100 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 66 optimal weight: 0.0670 chunk 22 optimal weight: 0.7980 chunk 96 optimal weight: 0.3980 overall best weight: 0.4122 ------------------------------------------------------------------------------- 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 = 0.4305 r_free = 0.4305 target = 0.177175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.127376 restraints weight = 13171.757| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 3.20 r_work: 0.3619 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9759 Z= 0.135 Angle : 0.540 11.516 13151 Z= 0.279 Chirality : 0.041 0.146 1511 Planarity : 0.003 0.044 1635 Dihedral : 4.340 20.551 1287 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.68 % Allowed : 14.07 % Favored : 84.25 % 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: -1.29 (0.24), residues: 1177 helix: 0.13 (0.20), residues: 704 sheet: -1.54 (0.67), residues: 63 loop : -2.45 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1047 HIS 0.006 0.001 HIS A 676 PHE 0.021 0.001 PHE A1293 TYR 0.015 0.001 TYR A1301 ARG 0.006 0.000 ARG A 622 *********************** 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 118 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7210 (m-80) cc_final: 0.6335 (m-80) REVERT: A 133 ARG cc_start: 0.6770 (tmm160) cc_final: 0.6332 (tmm160) REVERT: A 152 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6832 (ptm160) REVERT: A 382 ASN cc_start: 0.8238 (m110) cc_final: 0.7539 (p0) REVERT: A 404 LYS cc_start: 0.8263 (mtpt) cc_final: 0.7765 (pttm) REVERT: A 434 GLU cc_start: 0.5947 (mt-10) cc_final: 0.5444 (mm-30) REVERT: A 463 ASP cc_start: 0.8341 (p0) cc_final: 0.7628 (t0) REVERT: A 524 TYR cc_start: 0.7274 (m-10) cc_final: 0.6667 (m-80) REVERT: A 588 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7585 (tp30) REVERT: A 776 ARG cc_start: 0.8254 (ptt90) cc_final: 0.7674 (ptt-90) REVERT: A 987 GLN cc_start: 0.8599 (tt0) cc_final: 0.8269 (tm-30) REVERT: A 1092 LEU cc_start: 0.7960 (mt) cc_final: 0.7692 (pp) REVERT: A 1267 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8262 (tp30) REVERT: A 1349 LEU cc_start: 0.8427 (tp) cc_final: 0.8144 (tp) REVERT: A 1356 ASP cc_start: 0.9105 (t70) cc_final: 0.8876 (m-30) outliers start: 18 outliers final: 14 residues processed: 110 average time/residue: 0.2155 time to fit residues: 34.4270 Evaluate side-chains 110 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 348 GLU Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 1015 TYR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A1262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.170194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.118967 restraints weight = 13446.892| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.27 r_work: 0.3509 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9759 Z= 0.255 Angle : 0.615 11.611 13151 Z= 0.323 Chirality : 0.045 0.186 1511 Planarity : 0.004 0.041 1635 Dihedral : 4.628 22.314 1287 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.86 % Allowed : 14.45 % Favored : 83.69 % 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: -1.60 (0.24), residues: 1177 helix: -0.13 (0.20), residues: 707 sheet: -2.17 (0.62), residues: 73 loop : -2.48 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 186 HIS 0.006 0.001 HIS A 676 PHE 0.022 0.002 PHE A1293 TYR 0.017 0.002 TYR A1097 ARG 0.003 0.000 ARG A 299 *********************** 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 117 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7249 (m-80) cc_final: 0.6398 (m-80) REVERT: A 152 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6947 (ptm160) REVERT: A 226 TYR cc_start: 0.8231 (m-10) cc_final: 0.7854 (m-80) REVERT: A 382 ASN cc_start: 0.8280 (m110) cc_final: 0.7498 (p0) REVERT: A 404 LYS cc_start: 0.8219 (mtpt) cc_final: 0.7654 (pttm) REVERT: A 407 LYS cc_start: 0.7123 (mttt) cc_final: 0.6805 (mtpt) REVERT: A 434 GLU cc_start: 0.6010 (mt-10) cc_final: 0.5392 (mm-30) REVERT: A 463 ASP cc_start: 0.8291 (p0) cc_final: 0.7542 (t0) REVERT: A 524 TYR cc_start: 0.7062 (m-10) cc_final: 0.6657 (m-80) REVERT: A 588 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7596 (tp30) REVERT: A 987 GLN cc_start: 0.8652 (tt0) cc_final: 0.8346 (tm-30) REVERT: A 1092 LEU cc_start: 0.7968 (mt) cc_final: 0.7678 (pp) REVERT: A 1118 ASN cc_start: 0.7235 (p0) cc_final: 0.6979 (p0) REVERT: A 1267 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8523 (mm-30) REVERT: A 1349 LEU cc_start: 0.8434 (tp) cc_final: 0.8170 (tp) REVERT: A 1356 ASP cc_start: 0.9166 (t70) cc_final: 0.8897 (m-30) outliers start: 20 outliers final: 15 residues processed: 112 average time/residue: 0.2295 time to fit residues: 36.7371 Evaluate side-chains 109 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 123 ILE Chi-restraints excluded: chain A residue 152 ARG 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 439 VAL 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 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 Chi-restraints excluded: chain A residue 1367 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 81 optimal weight: 0.4980 chunk 113 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 84 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 chunk 59 optimal weight: 20.0000 chunk 42 optimal weight: 0.1980 chunk 30 optimal weight: 0.0970 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 894 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.176040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.126229 restraints weight = 13278.956| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 3.19 r_work: 0.3597 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9759 Z= 0.139 Angle : 0.545 12.508 13151 Z= 0.283 Chirality : 0.042 0.237 1511 Planarity : 0.003 0.043 1635 Dihedral : 4.353 20.182 1287 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.21 % Allowed : 15.10 % Favored : 83.69 % 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: -1.21 (0.25), residues: 1177 helix: 0.19 (0.20), residues: 702 sheet: -2.00 (0.63), residues: 73 loop : -2.30 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 186 HIS 0.004 0.001 HIS A 892 PHE 0.026 0.001 PHE A1293 TYR 0.012 0.001 TYR A1301 ARG 0.003 0.000 ARG A 384 *********************** 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 118 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7144 (m-80) cc_final: 0.6303 (m-80) REVERT: A 133 ARG cc_start: 0.6771 (tmm160) cc_final: 0.6375 (tmm160) REVERT: A 152 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6834 (ptm160) REVERT: A 256 LYS cc_start: 0.7178 (mmtt) cc_final: 0.6887 (mtpt) REVERT: A 382 ASN cc_start: 0.8289 (m110) cc_final: 0.7508 (p0) REVERT: A 404 LYS cc_start: 0.8209 (mtpt) cc_final: 0.7650 (pttm) REVERT: A 407 LYS cc_start: 0.7138 (mttt) cc_final: 0.6794 (mtpt) REVERT: A 434 GLU cc_start: 0.6071 (mt-10) cc_final: 0.5547 (mm-30) REVERT: A 463 ASP cc_start: 0.8294 (p0) cc_final: 0.7551 (t0) REVERT: A 524 TYR cc_start: 0.7124 (m-10) cc_final: 0.6587 (m-80) REVERT: A 588 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7671 (tp30) REVERT: A 987 GLN cc_start: 0.8567 (tt0) cc_final: 0.8275 (tm-30) REVERT: A 1092 LEU cc_start: 0.7981 (mt) cc_final: 0.7698 (pp) REVERT: A 1267 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8510 (mm-30) REVERT: A 1349 LEU cc_start: 0.8428 (tp) cc_final: 0.8150 (tp) REVERT: A 1356 ASP cc_start: 0.9121 (t70) cc_final: 0.8874 (m-30) outliers start: 13 outliers final: 10 residues processed: 114 average time/residue: 0.2264 time to fit residues: 36.5762 Evaluate side-chains 112 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 348 GLU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 422 ILE 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 1367 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 48 optimal weight: 0.0060 chunk 16 optimal weight: 0.0010 chunk 99 optimal weight: 0.9990 chunk 110 optimal weight: 0.0370 chunk 30 optimal weight: 0.6980 chunk 37 optimal weight: 0.0770 chunk 91 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.1638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.179357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.129831 restraints weight = 13218.217| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 3.27 r_work: 0.3646 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9759 Z= 0.127 Angle : 0.539 13.219 13151 Z= 0.272 Chirality : 0.041 0.240 1511 Planarity : 0.003 0.044 1635 Dihedral : 4.122 23.255 1287 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.12 % Allowed : 15.00 % Favored : 83.88 % 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: -0.87 (0.25), residues: 1177 helix: 0.47 (0.20), residues: 698 sheet: -1.44 (0.70), residues: 63 loop : -2.22 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 186 HIS 0.003 0.001 HIS A 443 PHE 0.026 0.001 PHE A1293 TYR 0.012 0.001 TYR A1097 ARG 0.003 0.000 ARG A 384 ********************** 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 121 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 1.158 Fit side-chains revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7062 (m-80) cc_final: 0.6232 (m-80) REVERT: A 133 ARG cc_start: 0.6838 (tmm160) cc_final: 0.6450 (ttp80) REVERT: A 152 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6759 (ptm160) REVERT: A 256 LYS cc_start: 0.7223 (mmtt) cc_final: 0.6949 (mtpt) REVERT: A 382 ASN cc_start: 0.8352 (m110) cc_final: 0.7599 (p0) REVERT: A 404 LYS cc_start: 0.8210 (mtpt) cc_final: 0.7634 (pttm) REVERT: A 434 GLU cc_start: 0.5957 (mt-10) cc_final: 0.5555 (mm-30) REVERT: A 463 ASP cc_start: 0.8265 (p0) cc_final: 0.7460 (t0) REVERT: A 524 TYR cc_start: 0.7030 (m-10) cc_final: 0.6464 (m-80) REVERT: A 588 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7657 (tp30) REVERT: A 916 MET cc_start: 0.8025 (tpt) cc_final: 0.7749 (tpp) REVERT: A 993 MET cc_start: 0.7911 (tpp) cc_final: 0.7625 (mmm) REVERT: A 1092 LEU cc_start: 0.7952 (mt) cc_final: 0.7677 (pp) REVERT: A 1267 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8535 (mm-30) REVERT: A 1356 ASP cc_start: 0.9115 (t70) cc_final: 0.8835 (m-30) outliers start: 12 outliers final: 9 residues processed: 117 average time/residue: 0.2125 time to fit residues: 35.7921 Evaluate side-chains 107 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 348 GLU Chi-restraints excluded: chain A residue 422 ILE 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 1367 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 39 optimal weight: 0.0770 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- 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 = 0.4271 r_free = 0.4271 target = 0.173408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.122822 restraints weight = 13385.459| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 3.25 r_work: 0.3566 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9759 Z= 0.197 Angle : 0.581 12.592 13151 Z= 0.298 Chirality : 0.043 0.180 1511 Planarity : 0.003 0.038 1635 Dihedral : 4.257 21.536 1287 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.12 % Allowed : 15.94 % Favored : 82.95 % 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: -1.03 (0.24), residues: 1177 helix: 0.34 (0.20), residues: 701 sheet: -1.48 (0.71), residues: 63 loop : -2.31 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 186 HIS 0.003 0.001 HIS A 443 PHE 0.024 0.001 PHE A1293 TYR 0.016 0.001 TYR A1097 ARG 0.004 0.000 ARG A 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5077.50 seconds wall clock time: 90 minutes 49.28 seconds (5449.28 seconds total)