Starting phenix.real_space_refine on Wed Apr 30 16:35:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jw4_36679/04_2025/8jw4_36679_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jw4_36679/04_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_36679/04_2025/8jw4_36679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jw4_36679/04_2025/8jw4_36679.map" model { file = "/net/cci-nas-00/data/ceres_data/8jw4_36679/04_2025/8jw4_36679_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jw4_36679/04_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 5.35, per 1000 atoms: 0.56 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: 2.58 Conformation dependent library (CDL) restraints added in 1.1 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: 1.07 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: 3.19 Time building geometry restraints manager: 2.81 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: 1.040 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.990 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: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.710 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.19593 ( 411) hydrogen bonds : angle 6.41524 ( 1188) covalent geometry : bond 0.00501 ( 9759) covalent geometry : angle 0.75521 (13151) *********************** 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 : 0.971 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: 0.2477 time to fit residues: 75.3653 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 : 0.998 ------------------------------------------------------------------------------- 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 = 0.130867 restraints weight = 12871.540| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 3.19 r_work: 0.3664 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 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= 0.149 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 Details of bonding type rmsd hydrogen bonds : bond 0.06043 ( 411) hydrogen bonds : angle 4.58861 ( 1188) covalent geometry : bond 0.00327 ( 9759) covalent geometry : angle 0.63791 (13151) *********************** 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 : 1.097 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: 0.7539 (m-80) cc_final: 0.7310 (m-80) REVERT: A 89 ASP cc_start: 0.6267 (OUTLIER) cc_final: 0.6003 (p0) REVERT: A 375 ILE cc_start: 0.3981 (mt) cc_final: 0.3682 (mp) REVERT: A 379 GLU cc_start: 0.6474 (tm-30) cc_final: 0.5775 (tm-30) REVERT: A 382 ASN cc_start: 0.8356 (m110) cc_final: 0.7675 (p0) REVERT: A 404 LYS cc_start: 0.8197 (mtpt) cc_final: 0.7788 (ptpt) REVERT: A 434 GLU cc_start: 0.6084 (mt-10) cc_final: 0.5809 (mm-30) REVERT: A 456 LYS cc_start: 0.4728 (mmtp) cc_final: 0.3692 (pttm) REVERT: A 463 ASP cc_start: 0.8251 (p0) cc_final: 0.7503 (t0) REVERT: A 524 TYR cc_start: 0.7197 (m-10) cc_final: 0.6912 (m-10) REVERT: A 588 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7688 (tp30) REVERT: A 622 ARG cc_start: 0.8178 (ttp-110) cc_final: 0.7833 (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: 0.8578 (mm-30) cc_final: 0.7939 (tp30) REVERT: A 1356 ASP cc_start: 0.9122 (t70) cc_final: 0.8896 (m-30) outliers start: 11 outliers final: 7 residues processed: 137 average time/residue: 0.2370 time to fit residues: 45.4523 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 : 1.023 ------------------------------------------------------------------------------- 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: 0.5980 chunk 21 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 ASN ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.178142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.128313 restraints weight = 13112.010| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 3.27 r_work: 0.3628 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9759 Z= 0.127 Angle : 0.575 9.256 13151 Z= 0.303 Chirality : 0.043 0.163 1511 Planarity : 0.004 0.041 1635 Dihedral : 4.867 22.755 1287 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.21 % Allowed : 10.25 % Favored : 88.54 % 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: 707 sheet: -3.08 (0.54), residues: 64 loop : -2.71 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1047 HIS 0.004 0.001 HIS A 892 PHE 0.012 0.001 PHE A 43 TYR 0.018 0.001 TYR A1097 ARG 0.006 0.000 ARG A1371 Details of bonding type rmsd hydrogen bonds : bond 0.05415 ( 411) hydrogen bonds : angle 4.22879 ( 1188) covalent geometry : bond 0.00273 ( 9759) covalent geometry : angle 0.57539 (13151) *********************** 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 : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7440 (m-80) cc_final: 0.6694 (m-80) REVERT: A 382 ASN cc_start: 0.8431 (m110) cc_final: 0.7773 (p0) REVERT: A 404 LYS cc_start: 0.8141 (mtpt) cc_final: 0.7759 (ptpt) REVERT: A 434 GLU cc_start: 0.6068 (mt-10) cc_final: 0.5799 (mm-30) REVERT: A 463 ASP cc_start: 0.8287 (p0) cc_final: 0.7593 (t0) REVERT: A 524 TYR cc_start: 0.7093 (m-10) cc_final: 0.6681 (m-80) REVERT: A 588 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7290 (tm-30) REVERT: A 776 ARG cc_start: 0.8167 (ptt90) cc_final: 0.7582 (ptt-90) REVERT: A 861 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8068 (ttmt) REVERT: A 916 MET cc_start: 0.8111 (tpt) cc_final: 0.7891 (tpt) REVERT: A 987 GLN cc_start: 0.8593 (tt0) cc_final: 0.7841 (tm-30) REVERT: A 1011 LYS cc_start: 0.5780 (mmmt) cc_final: 0.5544 (tppt) REVERT: A 1256 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7479 (mm110) REVERT: A 1267 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8067 (tp30) REVERT: A 1356 ASP cc_start: 0.9105 (t70) cc_final: 0.8895 (m-30) outliers start: 13 outliers final: 5 residues processed: 123 average time/residue: 0.2236 time to fit residues: 39.3883 Evaluate side-chains 102 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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: 0.9980 chunk 50 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 99 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A1256 GLN A1262 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.174731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.124359 restraints weight = 12964.556| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.23 r_work: 0.3581 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9759 Z= 0.135 Angle : 0.570 9.683 13151 Z= 0.302 Chirality : 0.043 0.151 1511 Planarity : 0.004 0.042 1635 Dihedral : 4.783 22.395 1287 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.12 % Allowed : 12.12 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.07 (0.24), residues: 1177 helix: -0.49 (0.20), residues: 712 sheet: -2.62 (0.58), residues: 64 loop : -2.67 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1047 HIS 0.004 0.001 HIS A 892 PHE 0.024 0.001 PHE A1293 TYR 0.019 0.001 TYR A1097 ARG 0.004 0.000 ARG A1371 Details of bonding type rmsd hydrogen bonds : bond 0.05373 ( 411) hydrogen bonds : angle 4.09511 ( 1188) covalent geometry : bond 0.00301 ( 9759) covalent geometry : angle 0.56975 (13151) *********************** 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: 12 poor density : 108 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7376 (m-80) cc_final: 0.6505 (m-80) REVERT: A 226 TYR cc_start: 0.8157 (m-10) cc_final: 0.7885 (m-80) REVERT: A 330 MET cc_start: 0.7745 (mmt) cc_final: 0.7352 (mmt) REVERT: A 382 ASN cc_start: 0.8200 (m110) cc_final: 0.7438 (p0) REVERT: A 404 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7733 (ptpt) REVERT: A 434 GLU cc_start: 0.6102 (mt-10) cc_final: 0.5769 (mm-30) REVERT: A 463 ASP cc_start: 0.8328 (p0) cc_final: 0.7602 (t0) REVERT: A 524 TYR cc_start: 0.7156 (m-10) cc_final: 0.6722 (m-80) REVERT: A 588 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7636 (tp30) REVERT: A 776 ARG cc_start: 0.8277 (ptt90) cc_final: 0.7760 (ptt-90) REVERT: A 987 GLN cc_start: 0.8701 (tt0) cc_final: 0.8069 (tm-30) REVERT: A 1267 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8170 (tp30) REVERT: A 1287 PHE cc_start: 0.7756 (m-10) cc_final: 0.7549 (m-10) REVERT: A 1356 ASP cc_start: 0.9132 (t70) cc_final: 0.8904 (m-30) REVERT: A 1362 ASP cc_start: 0.8024 (p0) cc_final: 0.7586 (p0) outliers start: 12 outliers final: 8 residues processed: 116 average time/residue: 0.2219 time to fit residues: 36.7004 Evaluate side-chains 104 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 101 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 116 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A1256 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.175040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.124496 restraints weight = 12984.291| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 3.23 r_work: 0.3577 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9759 Z= 0.121 Angle : 0.545 10.166 13151 Z= 0.287 Chirality : 0.042 0.161 1511 Planarity : 0.003 0.043 1635 Dihedral : 4.648 21.603 1287 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.86 % Allowed : 12.77 % Favored : 85.37 % 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: -1.78 (0.24), residues: 1177 helix: -0.28 (0.20), residues: 713 sheet: -1.91 (0.63), residues: 59 loop : -2.63 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1047 HIS 0.003 0.001 HIS A 892 PHE 0.020 0.001 PHE A1293 TYR 0.021 0.001 TYR A1301 ARG 0.003 0.000 ARG A1389 Details of bonding type rmsd hydrogen bonds : bond 0.05005 ( 411) hydrogen bonds : angle 3.93779 ( 1188) covalent geometry : bond 0.00264 ( 9759) covalent geometry : angle 0.54547 (13151) *********************** 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 126 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7330 (m-80) cc_final: 0.6429 (m-80) REVERT: A 160 GLU cc_start: 0.8168 (tt0) cc_final: 0.7836 (tp30) REVERT: A 226 TYR cc_start: 0.8129 (m-10) cc_final: 0.7771 (m-80) REVERT: A 382 ASN cc_start: 0.8244 (m110) cc_final: 0.7542 (p0) REVERT: A 404 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7714 (ptpt) REVERT: A 434 GLU cc_start: 0.6164 (mt-10) cc_final: 0.5765 (mm-30) REVERT: A 463 ASP cc_start: 0.8321 (p0) cc_final: 0.7583 (t0) REVERT: A 524 TYR cc_start: 0.7136 (m-10) cc_final: 0.6716 (m-80) REVERT: A 588 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7549 (tp30) REVERT: A 776 ARG cc_start: 0.8265 (ptt90) cc_final: 0.7719 (ptt-90) REVERT: A 987 GLN cc_start: 0.8719 (tt0) cc_final: 0.8199 (tm-30) REVERT: A 1256 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7408 (mm110) REVERT: A 1267 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8095 (tp30) REVERT: A 1336 ASP cc_start: 0.6180 (p0) cc_final: 0.5386 (t0) REVERT: A 1356 ASP cc_start: 0.9139 (t70) cc_final: 0.8900 (m-30) outliers start: 20 outliers final: 13 residues processed: 118 average time/residue: 0.2144 time to fit residues: 36.4073 Evaluate side-chains 110 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 378 ILE 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 1367 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 46 optimal weight: 0.1980 chunk 102 optimal weight: 0.9980 chunk 2 optimal weight: 0.0670 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 80 optimal weight: 0.0170 chunk 107 optimal weight: 0.9990 overall best weight: 0.2556 ------------------------------------------------------------------------------- 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 = 0.4320 r_free = 0.4320 target = 0.178772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.129247 restraints weight = 12980.712| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 3.18 r_work: 0.3641 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9759 Z= 0.099 Angle : 0.510 10.751 13151 Z= 0.267 Chirality : 0.041 0.139 1511 Planarity : 0.003 0.045 1635 Dihedral : 4.379 20.226 1287 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.58 % Allowed : 13.42 % Favored : 85.00 % 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: -1.41 (0.24), residues: 1177 helix: 0.02 (0.20), residues: 710 sheet: -1.47 (0.68), residues: 59 loop : -2.53 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1047 HIS 0.004 0.001 HIS A 443 PHE 0.022 0.001 PHE A1293 TYR 0.015 0.001 TYR A1301 ARG 0.006 0.000 ARG A 622 Details of bonding type rmsd hydrogen bonds : bond 0.04128 ( 411) hydrogen bonds : angle 3.69687 ( 1188) covalent geometry : bond 0.00194 ( 9759) covalent geometry : angle 0.51033 (13151) *********************** 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 127 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7163 (m-80) cc_final: 0.6296 (m-80) REVERT: A 133 ARG cc_start: 0.6765 (tmm160) cc_final: 0.6322 (tmm160) REVERT: A 152 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6809 (ptm160) REVERT: A 382 ASN cc_start: 0.8244 (m110) cc_final: 0.7531 (p0) REVERT: A 404 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7740 (pttm) REVERT: A 434 GLU cc_start: 0.6105 (mt-10) cc_final: 0.5781 (mm-30) REVERT: A 463 ASP cc_start: 0.8344 (p0) cc_final: 0.7616 (t0) REVERT: A 524 TYR cc_start: 0.7243 (m-10) cc_final: 0.6805 (m-80) REVERT: A 587 ASP cc_start: 0.6912 (t0) cc_final: 0.6707 (t0) REVERT: A 588 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7637 (tp30) REVERT: A 776 ARG cc_start: 0.8222 (ptt90) cc_final: 0.7649 (ptt-90) REVERT: A 916 MET cc_start: 0.8072 (tpt) cc_final: 0.7768 (tpp) REVERT: A 987 GLN cc_start: 0.8583 (tt0) cc_final: 0.8243 (tm-30) REVERT: A 1092 LEU cc_start: 0.7902 (mt) cc_final: 0.7649 (pp) REVERT: A 1267 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8221 (tp30) REVERT: A 1349 LEU cc_start: 0.8425 (tp) cc_final: 0.8158 (tp) REVERT: A 1356 ASP cc_start: 0.9124 (t70) cc_final: 0.8894 (m-30) outliers start: 17 outliers final: 11 residues processed: 119 average time/residue: 0.2225 time to fit residues: 37.5222 Evaluate side-chains 107 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 378 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 97 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 0.0170 chunk 73 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1256 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.176621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.126926 restraints weight = 13153.203| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 3.20 r_work: 0.3614 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9759 Z= 0.108 Angle : 0.531 11.044 13151 Z= 0.277 Chirality : 0.042 0.158 1511 Planarity : 0.003 0.044 1635 Dihedral : 4.306 20.776 1287 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.68 % Allowed : 13.89 % 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 (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: -1.26 (0.24), residues: 1177 helix: 0.12 (0.20), residues: 711 sheet: -1.14 (0.70), residues: 58 loop : -2.47 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1047 HIS 0.003 0.001 HIS A1400 PHE 0.020 0.001 PHE A1293 TYR 0.013 0.001 TYR A1097 ARG 0.005 0.000 ARG A 622 Details of bonding type rmsd hydrogen bonds : bond 0.04397 ( 411) hydrogen bonds : angle 3.71181 ( 1188) covalent geometry : bond 0.00229 ( 9759) covalent geometry : angle 0.53134 (13151) *********************** 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 : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7147 (m-80) cc_final: 0.6285 (m-80) REVERT: A 133 ARG cc_start: 0.6780 (tmm160) cc_final: 0.6344 (tmm160) REVERT: A 152 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6832 (ptm160) REVERT: A 256 LYS cc_start: 0.7191 (mmtt) cc_final: 0.6934 (mtpt) REVERT: A 382 ASN cc_start: 0.8198 (m110) cc_final: 0.7438 (p0) REVERT: A 404 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7715 (pttm) REVERT: A 463 ASP cc_start: 0.8354 (p0) cc_final: 0.7627 (t0) REVERT: A 524 TYR cc_start: 0.7330 (m-10) cc_final: 0.6910 (m-80) REVERT: A 588 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7651 (tp30) REVERT: A 776 ARG cc_start: 0.8257 (ptt90) cc_final: 0.7684 (ptt-90) REVERT: A 987 GLN cc_start: 0.8614 (tt0) cc_final: 0.8285 (tm-30) REVERT: A 988 GLU cc_start: 0.7658 (tt0) cc_final: 0.7420 (tp30) REVERT: A 1092 LEU cc_start: 0.7954 (mt) cc_final: 0.7688 (pp) REVERT: A 1267 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8266 (tp30) REVERT: A 1336 ASP cc_start: 0.5892 (OUTLIER) cc_final: 0.5550 (p0) REVERT: A 1356 ASP cc_start: 0.9109 (t70) cc_final: 0.8831 (m-30) outliers start: 18 outliers final: 13 residues processed: 111 average time/residue: 0.2138 time to fit residues: 34.0054 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 : 1.056 ------------------------------------------------------------------------------- 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 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 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 1367 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 40 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 114 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 894 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.173398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.122760 restraints weight = 13392.030| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 3.21 r_work: 0.3559 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9759 Z= 0.132 Angle : 0.581 11.932 13151 Z= 0.299 Chirality : 0.043 0.163 1511 Planarity : 0.003 0.042 1635 Dihedral : 4.383 21.115 1287 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.96 % Allowed : 13.70 % 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: -1.27 (0.24), residues: 1177 helix: 0.12 (0.20), residues: 705 sheet: -0.97 (0.72), residues: 58 loop : -2.50 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 186 HIS 0.004 0.001 HIS A 676 PHE 0.020 0.001 PHE A1293 TYR 0.016 0.001 TYR A1097 ARG 0.002 0.000 ARG A1371 Details of bonding type rmsd hydrogen bonds : bond 0.04981 ( 411) hydrogen bonds : angle 3.79052 ( 1188) covalent geometry : bond 0.00296 ( 9759) covalent geometry : angle 0.58090 (13151) *********************** 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 121 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7188 (m-80) cc_final: 0.6316 (m-80) REVERT: A 133 ARG cc_start: 0.6791 (tmm160) cc_final: 0.6344 (tmm160) REVERT: A 152 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6860 (ptm160) REVERT: A 256 LYS cc_start: 0.7239 (mmtt) cc_final: 0.6930 (mtpt) REVERT: A 382 ASN cc_start: 0.8297 (m110) cc_final: 0.7536 (p0) REVERT: A 404 LYS cc_start: 0.8190 (mtpt) cc_final: 0.7642 (pttm) REVERT: A 407 LYS cc_start: 0.7185 (mttt) cc_final: 0.6888 (mttt) REVERT: A 434 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5606 (mm-30) REVERT: A 463 ASP cc_start: 0.8355 (p0) cc_final: 0.7628 (t0) REVERT: A 524 TYR cc_start: 0.7219 (m-10) cc_final: 0.6594 (m-80) REVERT: A 588 GLU cc_start: 0.8529 (mt-10) cc_final: 0.7556 (tm-30) REVERT: A 987 GLN cc_start: 0.8678 (tt0) cc_final: 0.8408 (tm-30) REVERT: A 1092 LEU cc_start: 0.7988 (mt) cc_final: 0.7707 (pp) REVERT: A 1118 ASN cc_start: 0.7145 (p0) cc_final: 0.6892 (p0) REVERT: A 1267 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8306 (tp30) REVERT: A 1336 ASP cc_start: 0.5966 (OUTLIER) cc_final: 0.5549 (p0) REVERT: A 1356 ASP cc_start: 0.9119 (t70) cc_final: 0.8829 (m-30) outliers start: 21 outliers final: 15 residues processed: 114 average time/residue: 0.2110 time to fit residues: 34.4756 Evaluate side-chains 114 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 388 ASP 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 81 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 6 optimal weight: 0.0570 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 59 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.175560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.125655 restraints weight = 13284.967| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.19 r_work: 0.3592 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.4385 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= 0.107 Angle : 0.544 12.626 13151 Z= 0.280 Chirality : 0.042 0.151 1511 Planarity : 0.003 0.043 1635 Dihedral : 4.319 20.220 1287 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.12 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 (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: -1.14 (0.25), residues: 1177 helix: 0.24 (0.20), residues: 704 sheet: -1.54 (0.66), residues: 68 loop : -2.36 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1047 HIS 0.003 0.001 HIS A 892 PHE 0.022 0.001 PHE A1293 TYR 0.014 0.001 TYR A1097 ARG 0.005 0.000 ARG A 384 Details of bonding type rmsd hydrogen bonds : bond 0.04476 ( 411) hydrogen bonds : angle 3.70274 ( 1188) covalent geometry : bond 0.00226 ( 9759) covalent geometry : angle 0.54425 (13151) *********************** 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: 20 poor density : 98 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7141 (m-80) cc_final: 0.6280 (m-80) REVERT: A 133 ARG cc_start: 0.6792 (tmm160) cc_final: 0.6395 (tmm160) REVERT: A 152 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6850 (ptm160) REVERT: A 256 LYS cc_start: 0.7204 (mmtt) cc_final: 0.6922 (mtpt) REVERT: A 382 ASN cc_start: 0.8319 (m110) cc_final: 0.7542 (p0) REVERT: A 404 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7703 (pttm) REVERT: A 407 LYS cc_start: 0.7206 (mttt) cc_final: 0.6905 (mttt) REVERT: A 434 GLU cc_start: 0.5941 (mt-10) cc_final: 0.5423 (mm-30) REVERT: A 463 ASP cc_start: 0.8355 (p0) cc_final: 0.7628 (t0) REVERT: A 524 TYR cc_start: 0.7130 (m-10) cc_final: 0.6709 (m-80) REVERT: A 588 GLU cc_start: 0.8421 (mt-10) cc_final: 0.7630 (tp30) REVERT: A 987 GLN cc_start: 0.8577 (tt0) cc_final: 0.8311 (tm-30) REVERT: A 1092 LEU cc_start: 0.7981 (mt) cc_final: 0.7694 (pp) REVERT: A 1267 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8303 (tp30) REVERT: A 1356 ASP cc_start: 0.9112 (t70) cc_final: 0.8824 (m-30) outliers start: 20 outliers final: 17 residues processed: 108 average time/residue: 0.2140 time to fit residues: 33.2857 Evaluate side-chains 114 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1336 ASP Chi-restraints excluded: chain A residue 1367 THR Chi-restraints excluded: chain A residue 1402 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 43 optimal weight: 5.9990 chunk 80 optimal weight: 0.0970 chunk 31 optimal weight: 0.6980 chunk 48 optimal weight: 0.0770 chunk 16 optimal weight: 0.0870 chunk 99 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 91 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 overall best weight: 0.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.179456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.130059 restraints weight = 13259.246| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 3.27 r_work: 0.3644 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9759 Z= 0.098 Angle : 0.519 13.062 13151 Z= 0.266 Chirality : 0.041 0.170 1511 Planarity : 0.003 0.045 1635 Dihedral : 4.080 23.373 1287 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.40 % Allowed : 14.26 % 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: -0.83 (0.25), residues: 1177 helix: 0.50 (0.20), residues: 700 sheet: -0.98 (0.74), residues: 58 loop : -2.30 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 186 HIS 0.005 0.001 HIS A 892 PHE 0.022 0.001 PHE A1293 TYR 0.009 0.001 TYR A1097 ARG 0.003 0.000 ARG A 384 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 411) hydrogen bonds : angle 3.54081 ( 1188) covalent geometry : bond 0.00195 ( 9759) covalent geometry : angle 0.51880 (13151) ********************** 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 122 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7071 (m-80) cc_final: 0.6200 (m-80) REVERT: A 133 ARG cc_start: 0.6799 (tmm160) cc_final: 0.6439 (ttp80) REVERT: A 152 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6810 (ptm160) REVERT: A 351 ASN cc_start: 0.6695 (t160) cc_final: 0.6450 (t0) REVERT: A 382 ASN cc_start: 0.8350 (m110) cc_final: 0.7567 (p0) REVERT: A 404 LYS cc_start: 0.8229 (mtpt) cc_final: 0.7650 (pttm) REVERT: A 434 GLU cc_start: 0.5921 (mt-10) cc_final: 0.5568 (mm-30) REVERT: A 437 ILE cc_start: 0.7038 (mm) cc_final: 0.6772 (mm) REVERT: A 463 ASP cc_start: 0.8298 (p0) cc_final: 0.7512 (t0) REVERT: A 524 TYR cc_start: 0.7142 (m-10) cc_final: 0.6566 (m-80) REVERT: A 588 GLU cc_start: 0.8593 (mt-10) cc_final: 0.7527 (tm-30) REVERT: A 987 GLN cc_start: 0.8531 (tt0) cc_final: 0.8294 (tm-30) REVERT: A 993 MET cc_start: 0.8010 (tpp) cc_final: 0.7670 (mmm) REVERT: A 1092 LEU cc_start: 0.7949 (mt) cc_final: 0.7671 (pp) REVERT: A 1267 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8504 (mm-30) REVERT: A 1356 ASP cc_start: 0.9116 (t70) cc_final: 0.8835 (m-30) outliers start: 15 outliers final: 12 residues processed: 115 average time/residue: 0.2140 time to fit residues: 35.8288 Evaluate side-chains 110 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 378 ILE Chi-restraints excluded: chain A residue 422 ILE 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 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 8 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 40 optimal weight: 0.0040 chunk 102 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 39 optimal weight: 0.0050 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.4406 ------------------------------------------------------------------------------- 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 = 0.4310 r_free = 0.4310 target = 0.177848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.128371 restraints weight = 13249.848| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 3.26 r_work: 0.3619 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.4644 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= 0.101 Angle : 0.538 12.835 13151 Z= 0.273 Chirality : 0.042 0.178 1511 Planarity : 0.003 0.044 1635 Dihedral : 4.056 22.236 1287 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.40 % Allowed : 14.73 % 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: -0.71 (0.25), residues: 1177 helix: 0.62 (0.20), residues: 698 sheet: -0.89 (0.74), residues: 58 loop : -2.28 (0.27), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1047 HIS 0.003 0.001 HIS A 443 PHE 0.023 0.001 PHE A1005 TYR 0.013 0.001 TYR A1097 ARG 0.003 0.000 ARG A 384 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 411) hydrogen bonds : angle 3.52242 ( 1188) covalent geometry : bond 0.00215 ( 9759) covalent geometry : angle 0.53834 (13151) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5479.62 seconds wall clock time: 94 minutes 39.57 seconds (5679.57 seconds total)