Starting phenix.real_space_refine on Sun Dec 29 04:33:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jwg_36682/12_2024/8jwg_36682_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jwg_36682/12_2024/8jwg_36682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jwg_36682/12_2024/8jwg_36682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jwg_36682/12_2024/8jwg_36682.map" model { file = "/net/cci-nas-00/data/ceres_data/8jwg_36682/12_2024/8jwg_36682_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jwg_36682/12_2024/8jwg_36682_neut.cif" } resolution = 3.54 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= 0.054 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: 5 Type Number sf(0) Gaussians S 40 5.16 5 C 6241 2.51 5 N 1583 2.21 5 O 1750 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9620 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1192, 9594 Classifications: {'peptide': 1192} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 1165} 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 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'YMZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.80, per 1000 atoms: 0.60 Number of scatterers: 9620 At special positions: 0 Unit cell: (71.5, 111.1, 143, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 F 6 9.00 O 1750 8.00 N 1583 7.00 C 6241 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: 2.80 Conformation dependent library (CDL) restraints added in 1.2 seconds 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2262 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 4 sheets defined 64.8% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 27 through 39 removed outlier: 3.528A pdb=" N LEU A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.890A pdb=" N LEU A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 57 " --> pdb=" O HIS A 53 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 62 " --> pdb=" O PHE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 69 removed outlier: 5.121A pdb=" N SER A 67 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.726A pdb=" N SER A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 136 removed outlier: 3.503A pdb=" N ILE A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR A 114 " --> pdb=" O MET A 110 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 146 Processing helix chain 'A' and resid 148 through 163 removed outlier: 3.805A pdb=" N ARG A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 191 removed outlier: 4.065A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ILE A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 199 Processing helix chain 'A' and resid 202 through 240 removed outlier: 3.662A pdb=" N LYS A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASN A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N THR A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 250 through 305 removed outlier: 3.519A pdb=" N LEU A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS A 278 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 318 removed outlier: 3.557A pdb=" N SER A 318 " --> pdb=" O ASN A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 318' Processing helix chain 'A' and resid 319 through 330 removed outlier: 3.779A pdb=" N LEU A 323 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 336 through 358 removed outlier: 3.773A pdb=" N GLU A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ILE A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 444 through 448 Processing helix chain 'A' and resid 449 through 456 Processing helix chain 'A' and resid 472 through 477 removed outlier: 3.886A pdb=" N TYR A 477 " --> pdb=" O ASN A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 removed outlier: 5.077A pdb=" N LEU A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 487 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 523 Processing helix chain 'A' and resid 529 through 539 removed outlier: 4.194A pdb=" N VAL A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 539 " --> pdb=" O VAL A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 564 through 579 Processing helix chain 'A' and resid 594 through 607 removed outlier: 3.754A pdb=" N GLU A 598 " --> pdb=" O ASP A 594 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 626 removed outlier: 3.560A pdb=" N THR A 625 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A 626 " --> pdb=" O LEU A 623 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 622 through 626' Processing helix chain 'A' and resid 676 through 681 removed outlier: 4.001A pdb=" N MET A 680 " --> pdb=" O HIS A 676 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS A 681 " --> pdb=" O ASP A 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 676 through 681' Processing helix chain 'A' and resid 685 through 694 Processing helix chain 'A' and resid 772 through 783 removed outlier: 4.063A pdb=" N ILE A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 803 removed outlier: 3.532A pdb=" N VAL A 789 " --> pdb=" O TYR A 785 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 790 " --> pdb=" O LYS A 786 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE A 791 " --> pdb=" O LYS A 787 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 816 removed outlier: 3.767A pdb=" N LEU A 808 " --> pdb=" O PRO A 804 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 849 removed outlier: 3.961A pdb=" N ASN A 826 " --> pdb=" O ASN A 822 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE A 832 " --> pdb=" O ASN A 828 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR A 833 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 834 " --> pdb=" O TYR A 830 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 843 " --> pdb=" O ILE A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 873 removed outlier: 4.286A pdb=" N LYS A 858 " --> pdb=" O LYS A 854 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 859 " --> pdb=" O ILE A 855 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 860 " --> pdb=" O GLY A 856 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG A 865 " --> pdb=" O LYS A 861 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG A 866 " --> pdb=" O THR A 862 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 872 " --> pdb=" O PHE A 868 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR A 873 " --> pdb=" O GLU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 881 removed outlier: 3.850A pdb=" N PHE A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 881 " --> pdb=" O SER A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 905 removed outlier: 3.808A pdb=" N ILE A 893 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN A 894 " --> pdb=" O SER A 890 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL A 897 " --> pdb=" O ILE A 893 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 904 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 905 " --> pdb=" O LYS A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 927 removed outlier: 3.595A pdb=" N SER A 912 " --> pdb=" O ILE A 908 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET A 922 " --> pdb=" O PHE A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 945 removed outlier: 3.599A pdb=" N ALA A 933 " --> pdb=" O CYS A 929 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 962 removed outlier: 3.981A pdb=" N GLU A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 992 removed outlier: 3.649A pdb=" N GLU A 988 " --> pdb=" O PHE A 984 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE A 990 " --> pdb=" O ILE A 986 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1035 removed outlier: 4.512A pdb=" N TYR A1015 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS A1018 " --> pdb=" O ASP A1014 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLY A1019 " --> pdb=" O TYR A1015 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ARG A1022 " --> pdb=" O LYS A1018 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP A1031 " --> pdb=" O ASN A1027 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A1035 " --> pdb=" O TRP A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1055 removed outlier: 3.874A pdb=" N LEU A1052 " --> pdb=" O PHE A1048 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A1053 " --> pdb=" O GLY A1049 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG A1055 " --> pdb=" O PHE A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1081 removed outlier: 4.122A pdb=" N PHE A1063 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A1069 " --> pdb=" O LYS A1065 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE A1070 " --> pdb=" O SER A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1098 removed outlier: 3.859A pdb=" N GLU A1095 " --> pdb=" O LYS A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1102 Processing helix chain 'A' and resid 1169 through 1175 Processing helix chain 'A' and resid 1243 through 1248 removed outlier: 3.648A pdb=" N LEU A1247 " --> pdb=" O ASN A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1270 Processing helix chain 'A' and resid 1277 through 1288 removed outlier: 3.698A pdb=" N LYS A1286 " --> pdb=" O LYS A1282 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE A1287 " --> pdb=" O ARG A1283 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA A1288 " --> pdb=" O VAL A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1297 removed outlier: 4.026A pdb=" N LEU A1297 " --> pdb=" O ILE A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1310 Processing helix chain 'A' and resid 1313 through 1328 removed outlier: 3.698A pdb=" N LYS A1317 " --> pdb=" O SER A1313 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG A1328 " --> pdb=" O ARG A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1360 removed outlier: 3.896A pdb=" N LYS A1360 " --> pdb=" O ASP A1356 " (cutoff:3.500A) 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 407 through 408 removed outlier: 8.062A pdb=" N LYS A 407 " --> pdb=" O THR A 616 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 458 Processing sheet with id=AA3, first strand: chain 'A' and resid 1150 through 1151 removed outlier: 5.212A pdb=" N ILE A1128 " --> pdb=" O LEU A1233 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU A1233 " --> pdb=" O ILE A1128 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP A1130 " --> pdb=" O GLU A1231 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1332 through 1334 removed outlier: 6.214A pdb=" N THR A1157 " --> pdb=" O THR A1367 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA A1158 " --> pdb=" O VAL A1382 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N PHE A1384 " --> pdb=" O ALA A1158 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL A1160 " --> pdb=" O PHE A1384 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A1385 " --> pdb=" O PHE A1393 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A1393 " --> pdb=" O ASN A1385 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1272 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: 3.08 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: 2971 1.34 - 1.46: 1725 1.46 - 1.58: 5037 1.58 - 1.69: 0 1.69 - 1.81: 67 Bond restraints: 9800 Sorted by residual: bond pdb=" CAR YMZ A1500 " pdb=" NAP YMZ A1500 " ideal model delta sigma weight residual 1.298 1.374 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" CAJ YMZ A1500 " pdb=" CAU YMZ A1500 " ideal model delta sigma weight residual 1.414 1.372 0.042 2.00e-02 2.50e+03 4.52e+00 bond pdb=" CAS YMZ A1500 " pdb=" CAW YMZ A1500 " ideal model delta sigma weight residual 1.518 1.560 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" CAN YMZ A1500 " pdb=" NAQ YMZ A1500 " ideal model delta sigma weight residual 1.457 1.415 0.042 2.00e-02 2.50e+03 4.31e+00 bond pdb=" CAZ YMZ A1500 " pdb=" FAE YMZ A1500 " ideal model delta sigma weight residual 1.340 1.378 -0.038 2.00e-02 2.50e+03 3.56e+00 ... (remaining 9795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 12420 1.34 - 2.69: 670 2.69 - 4.03: 79 4.03 - 5.38: 31 5.38 - 6.72: 12 Bond angle restraints: 13212 Sorted by residual: angle pdb=" C ASN A 440 " pdb=" N ASP A 441 " pdb=" CA ASP A 441 " ideal model delta sigma weight residual 122.08 128.80 -6.72 1.47e+00 4.63e-01 2.09e+01 angle pdb=" C ALA A 821 " pdb=" N ASN A 822 " pdb=" CA ASN A 822 " ideal model delta sigma weight residual 121.54 127.62 -6.08 1.91e+00 2.74e-01 1.01e+01 angle pdb=" N LEU A1001 " pdb=" CA LEU A1001 " pdb=" C LEU A1001 " ideal model delta sigma weight residual 112.72 108.74 3.98 1.28e+00 6.10e-01 9.67e+00 angle pdb=" CA ASN A1106 " pdb=" CB ASN A1106 " pdb=" CG ASN A1106 " ideal model delta sigma weight residual 112.60 115.57 -2.97 1.00e+00 1.00e+00 8.79e+00 angle pdb=" C SER A1105 " pdb=" N ASN A1106 " pdb=" CA ASN A1106 " ideal model delta sigma weight residual 122.61 127.03 -4.42 1.56e+00 4.11e-01 8.04e+00 ... (remaining 13207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5720 17.92 - 35.84: 175 35.84 - 53.76: 18 53.76 - 71.68: 2 71.68 - 89.60: 3 Dihedral angle restraints: 5918 sinusoidal: 2413 harmonic: 3505 Sorted by residual: dihedral pdb=" CA TYR A1004 " pdb=" C TYR A1004 " pdb=" N PHE A1005 " pdb=" CA PHE A1005 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ARG A 776 " pdb=" C ARG A 776 " pdb=" N ILE A 777 " pdb=" CA ILE A 777 " ideal model delta harmonic sigma weight residual 180.00 159.44 20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA ARG A 428 " pdb=" C ARG A 428 " pdb=" N LEU A 429 " pdb=" CA LEU A 429 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 5915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 994 0.037 - 0.074: 376 0.074 - 0.111: 105 0.111 - 0.148: 33 0.148 - 0.185: 6 Chirality restraints: 1514 Sorted by residual: 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 2.83 -0.19 2.00e-01 2.50e+01 8.56e-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 7.83e-01 chirality pdb=" CAX YMZ A1500 " pdb=" CAO YMZ A1500 " pdb=" CAW YMZ A1500 " pdb=" NAQ YMZ A1500 " both_signs ideal model delta sigma weight residual False -2.39 -2.56 0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 1511 not shown) Planarity restraints: 1638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 290 " -0.019 2.00e-02 2.50e+03 1.38e-02 3.82e+00 pdb=" CG TYR A 290 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 290 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 290 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 290 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 290 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 290 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 290 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A1257 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A1258 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A1258 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1258 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 71 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO A 72 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " -0.026 5.00e-02 4.00e+02 ... (remaining 1635 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1463 2.76 - 3.29: 9996 3.29 - 3.83: 14263 3.83 - 4.36: 17239 4.36 - 4.90: 29001 Nonbonded interactions: 71962 Sorted by model distance: nonbonded pdb=" O ASN A 822 " pdb=" ND2 ASN A 826 " model vdw 2.223 3.120 nonbonded pdb=" OD2 ASP A 144 " pdb=" OH TYR A 430 " model vdw 2.232 3.040 nonbonded pdb=" O PRO A 338 " pdb=" OG1 THR A 341 " model vdw 2.234 3.040 nonbonded pdb=" O LYS A 220 " pdb=" OG SER A 223 " model vdw 2.246 3.040 nonbonded pdb=" NE ARG A1116 " pdb=" OD2 ASP A1246 " model vdw 2.267 3.120 ... (remaining 71957 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 group one per residue 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.760 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 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 0.076 9800 Z= 0.303 Angle : 0.721 6.724 13212 Z= 0.399 Chirality : 0.044 0.185 1514 Planarity : 0.004 0.049 1638 Dihedral : 9.433 89.598 3656 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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: -3.71 (0.20), residues: 1178 helix: -1.90 (0.16), residues: 658 sheet: -3.26 (0.73), residues: 34 loop : -3.12 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 186 HIS 0.010 0.002 HIS A 892 PHE 0.030 0.002 PHE A 926 TYR 0.033 0.002 TYR A 290 ARG 0.005 0.001 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.208 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8162 (tpp) cc_final: 0.7928 (tpp) REVERT: A 358 ASN cc_start: 0.6861 (m-40) cc_final: 0.6538 (t0) REVERT: A 793 PHE cc_start: 0.6511 (t80) cc_final: 0.6228 (t80) REVERT: A 880 ASP cc_start: 0.8342 (t70) cc_final: 0.8009 (t0) REVERT: A 1308 TYR cc_start: 0.7718 (m-80) cc_final: 0.7478 (m-80) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.3070 time to fit residues: 102.2152 Evaluate side-chains 111 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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: 5.9990 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 30 optimal weight: 0.1980 chunk 60 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 108 optimal weight: 0.0970 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 ASN A 894 ASN A 994 HIS A 998 ASN A1370 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 9800 Z= 0.344 Angle : 0.764 10.736 13212 Z= 0.405 Chirality : 0.050 0.187 1514 Planarity : 0.005 0.057 1638 Dihedral : 5.962 53.115 1307 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 2.14 % Allowed : 8.85 % Favored : 89.01 % 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: -2.91 (0.21), residues: 1178 helix: -1.12 (0.17), residues: 700 sheet: -3.21 (0.61), residues: 46 loop : -3.05 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP A 186 HIS 0.007 0.001 HIS A 898 PHE 0.026 0.002 PHE A 257 TYR 0.024 0.002 TYR A 290 ARG 0.004 0.001 ARG A1371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.101 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: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8462 (tpp) cc_final: 0.8052 (tpp) REVERT: A 358 ASN cc_start: 0.7294 (m-40) cc_final: 0.6649 (t0) REVERT: A 690 MET cc_start: 0.5129 (mmm) cc_final: 0.4617 (ptp) REVERT: A 793 PHE cc_start: 0.7133 (t80) cc_final: 0.6820 (t80) REVERT: A 1397 HIS cc_start: 0.8134 (t70) cc_final: 0.7391 (p-80) outliers start: 23 outliers final: 18 residues processed: 140 average time/residue: 0.2269 time to fit residues: 45.3491 Evaluate side-chains 114 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 926 PHE Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1412 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 0.2980 chunk 89 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 108 optimal weight: 0.3980 chunk 116 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN ** A1243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9800 Z= 0.171 Angle : 0.623 12.059 13212 Z= 0.318 Chirality : 0.043 0.168 1514 Planarity : 0.004 0.054 1638 Dihedral : 5.364 50.295 1307 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.96 % Allowed : 11.27 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.85 (0.23), residues: 1178 helix: -0.26 (0.19), residues: 685 sheet: -2.07 (0.70), residues: 45 loop : -2.64 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 453 HIS 0.003 0.001 HIS A 898 PHE 0.019 0.001 PHE A 941 TYR 0.016 0.001 TYR A1097 ARG 0.002 0.000 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.168 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: symmetry clash REVERT: A 358 ASN cc_start: 0.7223 (m-40) cc_final: 0.6599 (t0) REVERT: A 382 ASN cc_start: 0.7920 (t0) cc_final: 0.7709 (t0) REVERT: A 399 LEU cc_start: 0.7364 (tp) cc_final: 0.7114 (mm) REVERT: A 542 HIS cc_start: 0.6229 (p-80) cc_final: 0.5538 (p-80) REVERT: A 690 MET cc_start: 0.5145 (mmm) cc_final: 0.4576 (ptp) REVERT: A 988 GLU cc_start: 0.7676 (pp20) cc_final: 0.7261 (tm-30) REVERT: A 1242 TYR cc_start: 0.5324 (m-80) cc_final: 0.5121 (m-10) REVERT: A 1335 LEU cc_start: 0.8899 (mt) cc_final: 0.8461 (tt) REVERT: A 1397 HIS cc_start: 0.7973 (t70) cc_final: 0.7360 (p-80) outliers start: 21 outliers final: 14 residues processed: 132 average time/residue: 0.2358 time to fit residues: 43.4551 Evaluate side-chains 114 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 926 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1412 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 108 optimal weight: 0.0000 chunk 115 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 95 optimal weight: 0.0070 overall best weight: 0.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 870 ASN ** A1243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9800 Z= 0.151 Angle : 0.577 9.470 13212 Z= 0.299 Chirality : 0.042 0.167 1514 Planarity : 0.004 0.054 1638 Dihedral : 4.933 45.790 1307 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.14 % Allowed : 12.66 % Favored : 85.20 % 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: -1.19 (0.24), residues: 1178 helix: 0.25 (0.20), residues: 684 sheet: -0.93 (0.88), residues: 35 loop : -2.42 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 452 HIS 0.002 0.001 HIS A 898 PHE 0.015 0.001 PHE A1033 TYR 0.013 0.001 TYR A 290 ARG 0.004 0.000 ARG A1319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ASN cc_start: 0.7357 (m-40) cc_final: 0.6610 (t0) REVERT: A 399 LEU cc_start: 0.7378 (tp) cc_final: 0.7089 (mm) REVERT: A 690 MET cc_start: 0.5387 (mmm) cc_final: 0.4786 (ptp) REVERT: A 988 GLU cc_start: 0.7577 (pp20) cc_final: 0.7263 (tm-30) REVERT: A 1150 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7779 (t) REVERT: A 1335 LEU cc_start: 0.8862 (mt) cc_final: 0.8376 (tt) REVERT: A 1397 HIS cc_start: 0.7898 (OUTLIER) cc_final: 0.7387 (p-80) outliers start: 23 outliers final: 15 residues processed: 125 average time/residue: 0.2324 time to fit residues: 41.6030 Evaluate side-chains 111 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 926 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1150 THR Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1412 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.0870 chunk 1 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 ASN ** A1243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9800 Z= 0.199 Angle : 0.598 11.653 13212 Z= 0.311 Chirality : 0.043 0.202 1514 Planarity : 0.003 0.047 1638 Dihedral : 4.822 39.692 1307 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.42 % Allowed : 13.78 % Favored : 83.80 % 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: -1.15 (0.24), residues: 1178 helix: 0.33 (0.20), residues: 690 sheet: -1.29 (0.77), residues: 45 loop : -2.48 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 186 HIS 0.004 0.001 HIS A 898 PHE 0.014 0.001 PHE A 78 TYR 0.017 0.001 TYR A 290 ARG 0.004 0.000 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 LEU cc_start: 0.7483 (tp) cc_final: 0.7180 (mm) REVERT: A 542 HIS cc_start: 0.6056 (p-80) cc_final: 0.5381 (p-80) REVERT: A 690 MET cc_start: 0.5229 (mmm) cc_final: 0.4653 (ptp) REVERT: A 1150 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7757 (t) REVERT: A 1397 HIS cc_start: 0.7987 (OUTLIER) cc_final: 0.7447 (p-80) outliers start: 26 outliers final: 18 residues processed: 120 average time/residue: 0.2322 time to fit residues: 39.8146 Evaluate side-chains 114 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 926 PHE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1150 THR Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1412 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 9800 Z= 0.310 Angle : 0.702 12.386 13212 Z= 0.367 Chirality : 0.047 0.182 1514 Planarity : 0.004 0.039 1638 Dihedral : 5.130 29.512 1307 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.35 % Allowed : 13.31 % Favored : 83.33 % 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: -1.48 (0.23), residues: 1178 helix: 0.05 (0.19), residues: 682 sheet: -1.27 (0.76), residues: 45 loop : -2.57 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 186 HIS 0.007 0.001 HIS A 898 PHE 0.021 0.002 PHE A 78 TYR 0.026 0.002 TYR A 290 ARG 0.005 0.001 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 LEU cc_start: 0.7570 (tp) cc_final: 0.7265 (mm) REVERT: A 486 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7255 (tt0) REVERT: A 542 HIS cc_start: 0.6386 (p-80) cc_final: 0.5825 (p-80) REVERT: A 578 MET cc_start: 0.4345 (ttt) cc_final: 0.3605 (mmm) REVERT: A 690 MET cc_start: 0.5594 (mmm) cc_final: 0.4952 (ptm) REVERT: A 1150 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7799 (t) REVERT: A 1397 HIS cc_start: 0.8230 (OUTLIER) cc_final: 0.7571 (p-80) outliers start: 36 outliers final: 24 residues processed: 125 average time/residue: 0.2409 time to fit residues: 43.9407 Evaluate side-chains 119 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 926 PHE Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1150 THR Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1412 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 0.0020 chunk 84 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** A1243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9800 Z= 0.172 Angle : 0.610 12.566 13212 Z= 0.314 Chirality : 0.042 0.166 1514 Planarity : 0.003 0.040 1638 Dihedral : 4.752 25.586 1307 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.23 % Allowed : 15.08 % Favored : 82.68 % 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: -1.06 (0.24), residues: 1178 helix: 0.39 (0.20), residues: 690 sheet: -0.98 (0.78), residues: 45 loop : -2.45 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A1047 HIS 0.003 0.001 HIS A 898 PHE 0.011 0.001 PHE A 401 TYR 0.015 0.001 TYR A1242 ARG 0.003 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 LEU cc_start: 0.7517 (tp) cc_final: 0.7206 (mm) REVERT: A 542 HIS cc_start: 0.6237 (p-80) cc_final: 0.5816 (p-80) REVERT: A 578 MET cc_start: 0.4069 (ttt) cc_final: 0.3645 (mmm) REVERT: A 690 MET cc_start: 0.5560 (mmm) cc_final: 0.4941 (ptm) REVERT: A 916 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7232 (tpp) REVERT: A 1397 HIS cc_start: 0.8160 (t70) cc_final: 0.7500 (p-80) outliers start: 24 outliers final: 18 residues processed: 117 average time/residue: 0.2387 time to fit residues: 40.4991 Evaluate side-chains 116 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 916 MET Chi-restraints excluded: chain A residue 926 PHE Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1412 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9800 Z= 0.276 Angle : 0.676 13.199 13212 Z= 0.353 Chirality : 0.046 0.204 1514 Planarity : 0.004 0.038 1638 Dihedral : 4.895 20.947 1307 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.89 % Allowed : 14.62 % Favored : 82.50 % 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: -1.23 (0.23), residues: 1178 helix: 0.24 (0.19), residues: 687 sheet: -0.99 (0.78), residues: 45 loop : -2.50 (0.25), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 452 HIS 0.005 0.001 HIS A 898 PHE 0.018 0.001 PHE A 78 TYR 0.021 0.002 TYR A 290 ARG 0.004 0.000 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 LEU cc_start: 0.7563 (tp) cc_final: 0.7258 (mm) REVERT: A 542 HIS cc_start: 0.6296 (p-80) cc_final: 0.5900 (p-80) REVERT: A 578 MET cc_start: 0.4246 (ttt) cc_final: 0.3835 (mmm) REVERT: A 690 MET cc_start: 0.5633 (mmm) cc_final: 0.4995 (ptm) REVERT: A 916 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7307 (tpp) REVERT: A 1237 ILE cc_start: 0.7599 (mt) cc_final: 0.7369 (mp) REVERT: A 1397 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7584 (p-80) outliers start: 31 outliers final: 27 residues processed: 117 average time/residue: 0.2112 time to fit residues: 35.6622 Evaluate side-chains 121 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 916 MET Chi-restraints excluded: chain A residue 926 PHE Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1412 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 64 optimal weight: 0.0670 chunk 46 optimal weight: 0.4980 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 113 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9800 Z= 0.157 Angle : 0.610 13.524 13212 Z= 0.314 Chirality : 0.042 0.213 1514 Planarity : 0.003 0.038 1638 Dihedral : 4.499 18.730 1307 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.23 % Allowed : 15.18 % Favored : 82.59 % 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: -0.78 (0.24), residues: 1178 helix: 0.57 (0.20), residues: 691 sheet: -0.65 (0.80), residues: 45 loop : -2.29 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 452 HIS 0.003 0.001 HIS A 892 PHE 0.020 0.001 PHE A 411 TYR 0.019 0.001 TYR A1242 ARG 0.002 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.7547 (mmt) cc_final: 0.7196 (mmp) REVERT: A 399 LEU cc_start: 0.7629 (tp) cc_final: 0.7327 (mm) REVERT: A 480 TYR cc_start: 0.6794 (m-10) cc_final: 0.6413 (m-80) REVERT: A 542 HIS cc_start: 0.6200 (p-80) cc_final: 0.5868 (p-80) REVERT: A 578 MET cc_start: 0.4328 (ttt) cc_final: 0.4013 (mmm) REVERT: A 690 MET cc_start: 0.5651 (mmm) cc_final: 0.4986 (ptm) REVERT: A 899 LEU cc_start: 0.8079 (mm) cc_final: 0.7622 (tp) REVERT: A 916 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7221 (tpp) REVERT: A 1335 LEU cc_start: 0.8862 (mt) cc_final: 0.8445 (tp) REVERT: A 1397 HIS cc_start: 0.8217 (t70) cc_final: 0.7655 (p-80) outliers start: 24 outliers final: 18 residues processed: 118 average time/residue: 0.2249 time to fit residues: 38.0437 Evaluate side-chains 116 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 916 MET Chi-restraints excluded: chain A residue 926 PHE Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1412 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 74 optimal weight: 0.1980 chunk 100 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.5632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9800 Z= 0.216 Angle : 0.648 13.353 13212 Z= 0.336 Chirality : 0.044 0.220 1514 Planarity : 0.004 0.038 1638 Dihedral : 4.592 18.625 1307 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.86 % Allowed : 15.74 % Favored : 82.40 % 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: -0.88 (0.24), residues: 1178 helix: 0.48 (0.20), residues: 689 sheet: -0.59 (0.81), residues: 45 loop : -2.32 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 452 HIS 0.005 0.001 HIS A 898 PHE 0.018 0.001 PHE A 411 TYR 0.018 0.001 TYR A1242 ARG 0.008 0.000 ARG A 575 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 LEU cc_start: 0.7664 (tp) cc_final: 0.7367 (mm) REVERT: A 480 TYR cc_start: 0.6954 (m-10) cc_final: 0.6488 (m-80) REVERT: A 542 HIS cc_start: 0.6232 (p-80) cc_final: 0.5901 (p-80) REVERT: A 578 MET cc_start: 0.4330 (ttt) cc_final: 0.4014 (mmm) REVERT: A 690 MET cc_start: 0.5618 (mmm) cc_final: 0.4887 (ptm) REVERT: A 916 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7295 (tpp) REVERT: A 1259 MET cc_start: 0.8204 (mmm) cc_final: 0.7699 (tpt) REVERT: A 1397 HIS cc_start: 0.8267 (t70) cc_final: 0.7602 (p-80) outliers start: 20 outliers final: 19 residues processed: 111 average time/residue: 0.2195 time to fit residues: 35.8673 Evaluate side-chains 111 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 916 MET Chi-restraints excluded: chain A residue 926 PHE Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1412 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.164505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.123679 restraints weight = 17125.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.128436 restraints weight = 6750.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.131254 restraints weight = 3694.027| |-----------------------------------------------------------------------------| r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9800 Z= 0.158 Angle : 0.618 13.521 13212 Z= 0.318 Chirality : 0.043 0.253 1514 Planarity : 0.003 0.037 1638 Dihedral : 4.406 18.577 1307 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.77 % Allowed : 16.11 % Favored : 82.12 % 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: -0.66 (0.24), residues: 1178 helix: 0.66 (0.20), residues: 691 sheet: -0.39 (0.84), residues: 45 loop : -2.26 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 452 HIS 0.003 0.001 HIS A 898 PHE 0.020 0.001 PHE A 411 TYR 0.011 0.001 TYR A1242 ARG 0.007 0.000 ARG A 575 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2064.91 seconds wall clock time: 38 minutes 56.10 seconds (2336.10 seconds total)