Starting phenix.real_space_refine on Thu Mar 14 19:39:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jw4_36679/03_2024/8jw4_36679_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jw4_36679/03_2024/8jw4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jw4_36679/03_2024/8jw4_36679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jw4_36679/03_2024/8jw4_36679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jw4_36679/03_2024/8jw4_36679_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jw4_36679/03_2024/8jw4_36679_neut.pdb" } 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 Residue "A ARG 575": "NH1" <-> "NH2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A ARG 627": "NH1" <-> "NH2" Residue "A ARG 1138": "NH1" <-> "NH2" Residue "A ARG 1176": "NH1" <-> "NH2" Residue "A ARG 1371": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.27, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 3.25 Conformation dependent library (CDL) restraints added in 1.7 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: 1.16 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: 2.94 Time building geometry restraints manager: 3.62 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: 99.15 - 106.11: 130 106.11 - 113.07: 5236 113.07 - 120.03: 3654 120.03 - 126.99: 4074 126.99 - 133.95: 57 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 2.440 nonbonded pdb=" OD2 ASP A 144 " pdb=" OH TYR A 430 " model vdw 2.225 2.440 nonbonded pdb=" O ASN A 637 " pdb=" N ASN A 665 " model vdw 2.248 2.520 nonbonded pdb=" O ARG A 384 " pdb=" OG1 THR A 433 " model vdw 2.271 2.440 nonbonded pdb=" O LYS A 220 " pdb=" OG SER A 223 " model vdw 2.304 2.440 ... (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: 0.690 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: 4.010 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 27.450 Find NCS groups from input model: 0.260 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.510 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 223 time to evaluate : 1.027 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: 0.2456 time to fit residues: 74.4431 Evaluate side-chains 115 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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: 10.0000 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 48 optimal weight: 0.0370 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 overall best weight: 1.4062 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9759 Z= 0.252 Angle : 0.654 8.949 13151 Z= 0.346 Chirality : 0.046 0.183 1511 Planarity : 0.004 0.046 1635 Dihedral : 5.278 24.113 1287 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.30 % Allowed : 8.39 % Favored : 90.31 % 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: -3.07 (0.22), residues: 1177 helix: -1.27 (0.18), residues: 709 sheet: -3.61 (0.49), residues: 64 loop : -2.98 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1047 HIS 0.008 0.001 HIS A 892 PHE 0.016 0.002 PHE A 43 TYR 0.022 0.002 TYR A1097 ARG 0.008 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 143 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 GLU cc_start: 0.6374 (tm-30) cc_final: 0.5991 (tm-30) REVERT: A 382 ASN cc_start: 0.8154 (m110) cc_final: 0.7601 (p0) REVERT: A 404 LYS cc_start: 0.8307 (mtpt) cc_final: 0.7970 (ptpt) REVERT: A 434 GLU cc_start: 0.6026 (mt-10) cc_final: 0.5729 (mm-30) REVERT: A 463 ASP cc_start: 0.8422 (p0) cc_final: 0.7558 (t0) REVERT: A 520 MET cc_start: 0.5099 (mtm) cc_final: 0.4804 (ptm) REVERT: A 524 TYR cc_start: 0.7306 (m-10) cc_final: 0.7021 (m-10) REVERT: A 588 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7737 (tp30) REVERT: A 622 ARG cc_start: 0.8228 (ttp-110) cc_final: 0.8005 (tpp-160) REVERT: A 916 MET cc_start: 0.8082 (tpt) cc_final: 0.7821 (tpt) REVERT: A 987 GLN cc_start: 0.8238 (tt0) cc_final: 0.7740 (tm-30) REVERT: A 1267 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7842 (tp30) REVERT: A 1362 ASP cc_start: 0.7600 (p0) cc_final: 0.7042 (p0) outliers start: 14 outliers final: 8 residues processed: 139 average time/residue: 0.2243 time to fit residues: 43.4920 Evaluate side-chains 111 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 300 ILE Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 1150 THR Chi-restraints excluded: chain A residue 1236 ASP 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 60 optimal weight: 20.0000 chunk 33 optimal weight: 0.0040 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 116 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 107 optimal weight: 0.0270 chunk 36 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 overall best weight: 0.4250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 ASN A 892 HIS ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.2998 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= 0.143 Angle : 0.542 8.923 13151 Z= 0.284 Chirality : 0.042 0.164 1511 Planarity : 0.004 0.042 1635 Dihedral : 4.805 21.808 1287 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.12 % Allowed : 9.88 % Favored : 89.00 % 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: -2.28 (0.23), residues: 1177 helix: -0.61 (0.19), residues: 710 sheet: -2.99 (0.56), residues: 64 loop : -2.78 (0.27), residues: 403 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 202 TYR 0.017 0.001 TYR A1097 ARG 0.007 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 128 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7301 (m-80) cc_final: 0.6296 (m-80) REVERT: A 239 MET cc_start: 0.7634 (tpp) cc_final: 0.7080 (tpp) REVERT: A 382 ASN cc_start: 0.8120 (m110) cc_final: 0.7511 (p0) REVERT: A 404 LYS cc_start: 0.8305 (mtpt) cc_final: 0.7940 (ptpt) REVERT: A 463 ASP cc_start: 0.8468 (p0) cc_final: 0.7550 (t0) REVERT: A 520 MET cc_start: 0.5010 (mtm) cc_final: 0.4767 (ptm) REVERT: A 524 TYR cc_start: 0.7324 (m-10) cc_final: 0.6949 (m-10) REVERT: A 588 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7577 (tp30) REVERT: A 916 MET cc_start: 0.8050 (tpt) cc_final: 0.7847 (tpt) REVERT: A 987 GLN cc_start: 0.8455 (tt0) cc_final: 0.7970 (tm-30) REVERT: A 1011 LYS cc_start: 0.5966 (mmmt) cc_final: 0.5743 (tppt) REVERT: A 1267 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7923 (tp30) outliers start: 12 outliers final: 5 residues processed: 123 average time/residue: 0.2133 time to fit residues: 37.2694 Evaluate side-chains 100 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1150 THR Chi-restraints excluded: chain A residue 1367 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 115 optimal weight: 8.9990 chunk 102 optimal weight: 0.0470 chunk 30 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 overall best weight: 1.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A1020 GLN A1262 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9759 Z= 0.246 Angle : 0.608 9.275 13151 Z= 0.321 Chirality : 0.045 0.163 1511 Planarity : 0.004 0.040 1635 Dihedral : 4.872 23.201 1287 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.14 % Allowed : 11.37 % Favored : 86.49 % 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: -2.09 (0.24), residues: 1177 helix: -0.49 (0.20), residues: 711 sheet: -2.13 (0.62), residues: 59 loop : -2.81 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1047 HIS 0.003 0.001 HIS A 443 PHE 0.013 0.001 PHE A 43 TYR 0.020 0.002 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 132 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7400 (m-80) cc_final: 0.6324 (m-80) REVERT: A 256 LYS cc_start: 0.6996 (mmtt) cc_final: 0.6755 (mtpt) REVERT: A 382 ASN cc_start: 0.7926 (m110) cc_final: 0.7232 (p0) REVERT: A 404 LYS cc_start: 0.8324 (mtpt) cc_final: 0.7869 (ptpt) REVERT: A 463 ASP cc_start: 0.8552 (p0) cc_final: 0.7584 (t0) REVERT: A 520 MET cc_start: 0.4993 (mtm) cc_final: 0.4706 (ptm) REVERT: A 524 TYR cc_start: 0.7339 (m-10) cc_final: 0.6971 (m-10) REVERT: A 588 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7426 (tp30) REVERT: A 987 GLN cc_start: 0.8713 (tt0) cc_final: 0.8250 (tm-30) REVERT: A 1256 GLN cc_start: 0.8157 (mm110) cc_final: 0.7468 (mm-40) REVERT: A 1267 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8043 (tp30) REVERT: A 1336 ASP cc_start: 0.5981 (OUTLIER) cc_final: 0.5488 (p0) outliers start: 23 outliers final: 13 residues processed: 125 average time/residue: 0.2166 time to fit residues: 38.5471 Evaluate side-chains 108 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 300 ILE 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 1150 THR Chi-restraints excluded: chain A residue 1236 ASP Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1336 ASP 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 65 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9759 Z= 0.262 Angle : 0.615 9.229 13151 Z= 0.326 Chirality : 0.045 0.164 1511 Planarity : 0.004 0.039 1635 Dihedral : 4.952 22.809 1287 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.33 % Allowed : 12.86 % Favored : 84.81 % 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: -2.13 (0.24), residues: 1177 helix: -0.53 (0.19), residues: 717 sheet: -2.41 (0.61), residues: 69 loop : -2.76 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1047 HIS 0.003 0.001 HIS A 53 PHE 0.014 0.002 PHE A 43 TYR 0.020 0.002 TYR A1097 ARG 0.003 0.000 ARG A 384 *********************** 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 132 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7186 (m-80) cc_final: 0.5908 (m-80) REVERT: A 382 ASN cc_start: 0.7890 (m110) cc_final: 0.7287 (p0) REVERT: A 404 LYS cc_start: 0.8379 (mtpt) cc_final: 0.7861 (pttm) REVERT: A 407 LYS cc_start: 0.7365 (mttt) cc_final: 0.7079 (mtpt) REVERT: A 434 GLU cc_start: 0.6022 (mt-10) cc_final: 0.5586 (mm-30) REVERT: A 463 ASP cc_start: 0.8561 (p0) cc_final: 0.7543 (t0) REVERT: A 520 MET cc_start: 0.5087 (mtm) cc_final: 0.4558 (ptm) REVERT: A 588 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7447 (tp30) REVERT: A 987 GLN cc_start: 0.8679 (tt0) cc_final: 0.8374 (tm-30) REVERT: A 988 GLU cc_start: 0.7632 (tt0) cc_final: 0.7267 (tp30) REVERT: A 1242 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.8068 (m-10) REVERT: A 1256 GLN cc_start: 0.8207 (mm110) cc_final: 0.7873 (mm-40) REVERT: A 1267 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8138 (tp30) REVERT: A 1336 ASP cc_start: 0.6261 (OUTLIER) cc_final: 0.5871 (p0) outliers start: 25 outliers final: 14 residues processed: 125 average time/residue: 0.2331 time to fit residues: 40.4022 Evaluate side-chains 110 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 123 ILE Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 300 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 1150 THR Chi-restraints excluded: chain A residue 1236 ASP Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1336 ASP Chi-restraints excluded: chain A residue 1349 LEU 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 103 optimal weight: 0.9980 chunk 22 optimal weight: 0.0060 chunk 67 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 ASN A1256 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.4164 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= 0.157 Angle : 0.553 10.572 13151 Z= 0.287 Chirality : 0.042 0.140 1511 Planarity : 0.003 0.042 1635 Dihedral : 4.687 21.324 1287 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.96 % Allowed : 13.79 % 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: -1.71 (0.24), residues: 1177 helix: -0.20 (0.20), residues: 716 sheet: -2.04 (0.64), residues: 68 loop : -2.64 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1047 HIS 0.003 0.001 HIS A 443 PHE 0.012 0.001 PHE A 202 TYR 0.014 0.001 TYR A1097 ARG 0.005 0.000 ARG A1371 *********************** 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 fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.6969 (m-80) cc_final: 0.5781 (m-80) REVERT: A 160 GLU cc_start: 0.7892 (tp30) cc_final: 0.7657 (tp30) REVERT: A 256 LYS cc_start: 0.6882 (mmtt) cc_final: 0.6654 (mtpt) REVERT: A 382 ASN cc_start: 0.7972 (m110) cc_final: 0.7285 (p0) REVERT: A 404 LYS cc_start: 0.8391 (mtpt) cc_final: 0.7881 (pttm) REVERT: A 407 LYS cc_start: 0.7318 (mttt) cc_final: 0.7047 (mtpt) REVERT: A 434 GLU cc_start: 0.5988 (mt-10) cc_final: 0.5605 (mm-30) REVERT: A 520 MET cc_start: 0.5042 (mtm) cc_final: 0.4535 (ptm) REVERT: A 588 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7391 (tm-30) REVERT: A 776 ARG cc_start: 0.8240 (ptt90) cc_final: 0.7949 (ptt90) REVERT: A 1267 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8131 (tp30) outliers start: 21 outliers final: 15 residues processed: 116 average time/residue: 0.2088 time to fit residues: 35.0595 Evaluate side-chains 108 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 281 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 477 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 1150 THR Chi-restraints excluded: chain A residue 1236 ASP Chi-restraints excluded: chain A residue 1367 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 64 optimal weight: 0.0050 chunk 114 optimal weight: 0.0570 chunk 71 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.4712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.4289 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= 0.135 Angle : 0.541 11.280 13151 Z= 0.278 Chirality : 0.041 0.166 1511 Planarity : 0.003 0.043 1635 Dihedral : 4.507 20.757 1287 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % 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: -1.41 (0.24), residues: 1177 helix: 0.05 (0.20), residues: 708 sheet: -1.80 (0.65), residues: 68 loop : -2.53 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1047 HIS 0.003 0.001 HIS A 443 PHE 0.011 0.001 PHE A1287 TYR 0.013 0.001 TYR A1097 ARG 0.006 0.000 ARG A1371 *********************** 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 121 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.6951 (m-80) cc_final: 0.5766 (m-80) REVERT: A 133 ARG cc_start: 0.6426 (tmm160) cc_final: 0.6012 (tmm160) REVERT: A 160 GLU cc_start: 0.7892 (tp30) cc_final: 0.7651 (tp30) REVERT: A 382 ASN cc_start: 0.7961 (m110) cc_final: 0.7276 (p0) REVERT: A 404 LYS cc_start: 0.8360 (mtpt) cc_final: 0.7771 (ptpt) REVERT: A 434 GLU cc_start: 0.5858 (mt-10) cc_final: 0.5537 (mm-30) REVERT: A 520 MET cc_start: 0.5010 (mtm) cc_final: 0.4517 (ptm) REVERT: A 588 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7385 (tm-30) REVERT: A 987 GLN cc_start: 0.8638 (tp40) cc_final: 0.8273 (tp40) REVERT: A 1267 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8181 (tp30) outliers start: 20 outliers final: 16 residues processed: 113 average time/residue: 0.1960 time to fit residues: 31.8085 Evaluate side-chains 108 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1150 THR Chi-restraints excluded: chain A residue 1236 ASP 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 68 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 72 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9759 Z= 0.273 Angle : 0.623 11.233 13151 Z= 0.323 Chirality : 0.045 0.168 1511 Planarity : 0.004 0.039 1635 Dihedral : 4.757 22.760 1287 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.14 % Allowed : 14.91 % 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: -1.62 (0.24), residues: 1177 helix: -0.16 (0.20), residues: 714 sheet: -1.80 (0.65), residues: 68 loop : -2.56 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1047 HIS 0.003 0.001 HIS A 53 PHE 0.014 0.002 PHE A 842 TYR 0.021 0.002 TYR A1097 ARG 0.005 0.001 ARG A1371 *********************** 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 fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.6999 (m-80) cc_final: 0.5766 (m-80) REVERT: A 382 ASN cc_start: 0.7898 (m110) cc_final: 0.7209 (p0) REVERT: A 404 LYS cc_start: 0.8457 (mtpt) cc_final: 0.7868 (pttm) REVERT: A 407 LYS cc_start: 0.7252 (mttt) cc_final: 0.6986 (mtpt) REVERT: A 434 GLU cc_start: 0.6108 (mt-10) cc_final: 0.5578 (mm-30) REVERT: A 520 MET cc_start: 0.5099 (mtm) cc_final: 0.4570 (ptm) REVERT: A 588 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7378 (tm-30) REVERT: A 1267 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8329 (mm-30) outliers start: 23 outliers final: 19 residues processed: 111 average time/residue: 0.2204 time to fit residues: 34.9816 Evaluate side-chains 110 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1150 THR Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1236 ASP 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 106 optimal weight: 0.2980 chunk 109 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 96 optimal weight: 0.2980 chunk 101 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.4535 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= 0.147 Angle : 0.548 11.786 13151 Z= 0.280 Chirality : 0.042 0.169 1511 Planarity : 0.003 0.041 1635 Dihedral : 4.551 22.463 1287 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.86 % Allowed : 15.47 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.30 (0.24), residues: 1177 helix: 0.13 (0.20), residues: 708 sheet: -1.38 (0.73), residues: 58 loop : -2.51 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1047 HIS 0.003 0.001 HIS A 443 PHE 0.011 0.001 PHE A1287 TYR 0.012 0.001 TYR A1097 ARG 0.005 0.000 ARG A1371 *********************** 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 114 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.6949 (m-80) cc_final: 0.5745 (m-80) REVERT: A 133 ARG cc_start: 0.6353 (tmm160) cc_final: 0.5972 (tmm160) REVERT: A 235 GLU cc_start: 0.7652 (tt0) cc_final: 0.7214 (tm-30) REVERT: A 382 ASN cc_start: 0.7875 (m110) cc_final: 0.7239 (p0) REVERT: A 404 LYS cc_start: 0.8458 (mtpt) cc_final: 0.7861 (pttm) REVERT: A 407 LYS cc_start: 0.7272 (mttt) cc_final: 0.6867 (mtmt) REVERT: A 434 GLU cc_start: 0.5893 (mt-10) cc_final: 0.5519 (mm-30) REVERT: A 520 MET cc_start: 0.5042 (mtm) cc_final: 0.4541 (ptm) REVERT: A 588 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7433 (tm-30) REVERT: A 1267 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8323 (mm-30) REVERT: A 1336 ASP cc_start: 0.5784 (OUTLIER) cc_final: 0.5212 (p0) outliers start: 20 outliers final: 19 residues processed: 107 average time/residue: 0.2156 time to fit residues: 33.1655 Evaluate side-chains 111 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 SER 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 281 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1150 THR Chi-restraints excluded: chain A residue 1236 ASP 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 53 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 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 : 0.003 0.025 9759 Z= 0.178 Angle : 0.564 12.805 13151 Z= 0.288 Chirality : 0.043 0.181 1511 Planarity : 0.003 0.042 1635 Dihedral : 4.507 23.140 1287 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 1.96 % Allowed : 15.75 % Favored : 82.29 % 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: 0.15 (0.20), residues: 709 sheet: -1.32 (0.72), residues: 58 loop : -2.50 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1047 HIS 0.003 0.001 HIS A 443 PHE 0.010 0.001 PHE A 818 TYR 0.015 0.001 TYR A1097 ARG 0.005 0.000 ARG A1371 ********************** 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 116 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.6943 (m-80) cc_final: 0.5731 (m-80) REVERT: A 133 ARG cc_start: 0.6371 (tmm160) cc_final: 0.6013 (tmm160) REVERT: A 235 GLU cc_start: 0.7636 (tt0) cc_final: 0.7290 (tm-30) REVERT: A 382 ASN cc_start: 0.7980 (m110) cc_final: 0.7263 (p0) REVERT: A 404 LYS cc_start: 0.8446 (mtpt) cc_final: 0.7827 (pttm) REVERT: A 407 LYS cc_start: 0.7271 (mttt) cc_final: 0.7014 (mtpt) REVERT: A 434 GLU cc_start: 0.5919 (mt-10) cc_final: 0.5525 (mm-30) REVERT: A 520 MET cc_start: 0.5045 (mtm) cc_final: 0.4543 (ptm) REVERT: A 588 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7511 (tm-30) REVERT: A 776 ARG cc_start: 0.8200 (ptt90) cc_final: 0.7934 (ptt90) REVERT: A 987 GLN cc_start: 0.8919 (tp40) cc_final: 0.8329 (tp40) REVERT: A 1267 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8340 (mm-30) REVERT: A 1308 TYR cc_start: 0.8125 (m-80) cc_final: 0.6993 (m-80) outliers start: 21 outliers final: 19 residues processed: 110 average time/residue: 0.2151 time to fit residues: 33.9208 Evaluate side-chains 111 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1150 THR Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1236 ASP 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 87 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 97 optimal weight: 5.9990 chunk 11 optimal weight: 0.0370 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.4264 r_free = 0.4264 target = 0.173371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.123119 restraints weight = 12977.035| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 3.18 r_work: 0.3570 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.4676 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= 0.139 Angle : 0.536 12.780 13151 Z= 0.271 Chirality : 0.041 0.166 1511 Planarity : 0.003 0.042 1635 Dihedral : 4.341 23.747 1287 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.86 % Allowed : 16.03 % Favored : 82.11 % 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: -1.07 (0.25), residues: 1177 helix: 0.31 (0.20), residues: 707 sheet: -1.42 (0.69), residues: 63 loop : -2.41 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1047 HIS 0.003 0.001 HIS A 443 PHE 0.008 0.001 PHE A 818 TYR 0.013 0.001 TYR A1097 ARG 0.004 0.000 ARG A1371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2148.00 seconds wall clock time: 39 minutes 23.11 seconds (2363.11 seconds total)