Starting phenix.real_space_refine on Fri Mar 14 01:46:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wom_37692/03_2025/8wom_37692_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wom_37692/03_2025/8wom_37692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wom_37692/03_2025/8wom_37692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wom_37692/03_2025/8wom_37692.map" model { file = "/net/cci-nas-00/data/ceres_data/8wom_37692/03_2025/8wom_37692_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wom_37692/03_2025/8wom_37692_neut.cif" } resolution = 3.5 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= 0.006 sd= 0.096 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 38 5.16 5 C 5987 2.51 5 N 1583 2.21 5 O 1740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9348 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1217, 9314 Classifications: {'peptide': 1217} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 30, 'TRANS': 1186} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'BLD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.69, per 1000 atoms: 0.61 Number of scatterers: 9348 At special positions: 0 Unit cell: (73.7, 106.7, 144.1, 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 38 16.00 O 1740 8.00 N 1583 7.00 C 5987 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: 1.94 Conformation dependent library (CDL) restraints added in 1.3 seconds 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 6 sheets defined 47.2% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 46 through 51 removed outlier: 3.504A pdb=" N VAL A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 71 removed outlier: 4.165A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 98 removed outlier: 3.547A pdb=" N HIS A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 90 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 150 through 160 removed outlier: 3.565A pdb=" N VAL A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 176 removed outlier: 3.617A pdb=" N TYR A 169 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 184 Processing helix chain 'A' and resid 194 through 209 removed outlier: 3.916A pdb=" N PHE A 200 " --> pdb=" O PRO A 196 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 removed outlier: 4.392A pdb=" N LYS A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 4.670A pdb=" N ILE A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 254 through 263 removed outlier: 3.745A pdb=" N LYS A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 303 through 314 removed outlier: 3.867A pdb=" N ALA A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 309 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 319 removed outlier: 3.811A pdb=" N LEU A 318 " --> pdb=" O GLY A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.803A pdb=" N LYS A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 removed outlier: 4.033A pdb=" N GLU A 414 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 470 through 477 Processing helix chain 'A' and resid 511 through 520 removed outlier: 3.660A pdb=" N ALA A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 550 removed outlier: 3.994A pdb=" N VAL A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 545 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 605 Processing helix chain 'A' and resid 621 through 632 removed outlier: 3.606A pdb=" N HIS A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.556A pdb=" N ARG A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 677 " --> pdb=" O PHE A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 700 removed outlier: 3.847A pdb=" N ILE A 700 " --> pdb=" O SER A 697 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 697 through 700' Processing helix chain 'A' and resid 701 through 715 removed outlier: 3.695A pdb=" N ALA A 705 " --> pdb=" O GLY A 701 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 712 " --> pdb=" O MET A 708 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'A' and resid 728 through 737 removed outlier: 4.592A pdb=" N TYR A 734 " --> pdb=" O TYR A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 751 removed outlier: 3.544A pdb=" N TYR A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 751 " --> pdb=" O ILE A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 772 removed outlier: 3.993A pdb=" N ALA A 770 " --> pdb=" O MET A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 780 removed outlier: 4.157A pdb=" N PHE A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 785 removed outlier: 3.707A pdb=" N ASN A 785 " --> pdb=" O ASP A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 805 Processing helix chain 'A' and resid 808 through 813 Processing helix chain 'A' and resid 813 through 818 Processing helix chain 'A' and resid 820 through 829 removed outlier: 3.799A pdb=" N VAL A 824 " --> pdb=" O THR A 820 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A 825 " --> pdb=" O SER A 821 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE A 826 " --> pdb=" O PHE A 822 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 829 " --> pdb=" O ALA A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 853 Proline residue: A 841 - end of helix removed outlier: 3.575A pdb=" N LEU A 845 " --> pdb=" O PRO A 841 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 848 " --> pdb=" O VAL A 844 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 850 " --> pdb=" O ALA A 846 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLN A 851 " --> pdb=" O ASN A 847 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 852 " --> pdb=" O PHE A 848 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 853 " --> pdb=" O ALA A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 856 No H-bonds generated for 'chain 'A' and resid 854 through 856' Processing helix chain 'A' and resid 860 through 865 removed outlier: 4.186A pdb=" N ALA A 864 " --> pdb=" O ASP A 860 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N HIS A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 860 through 865' Processing helix chain 'A' and resid 866 through 875 removed outlier: 3.835A pdb=" N ILE A 871 " --> pdb=" O LYS A 867 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 883 Processing helix chain 'A' and resid 884 through 887 removed outlier: 4.043A pdb=" N ALA A 887 " --> pdb=" O ALA A 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 884 through 887' Processing helix chain 'A' and resid 891 through 895 Processing helix chain 'A' and resid 900 through 905 Processing helix chain 'A' and resid 908 through 921 removed outlier: 3.772A pdb=" N GLY A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A 921 " --> pdb=" O PHE A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 926 removed outlier: 3.663A pdb=" N TYR A 925 " --> pdb=" O GLN A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 939 removed outlier: 3.701A pdb=" N ILE A 931 " --> pdb=" O SER A 927 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 938 " --> pdb=" O TYR A 934 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 939 " --> pdb=" O GLY A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 959 removed outlier: 3.528A pdb=" N VAL A 955 " --> pdb=" O LYS A 951 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 964 removed outlier: 4.023A pdb=" N ALA A 964 " --> pdb=" O ALA A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 975 removed outlier: 4.002A pdb=" N ILE A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1059 removed outlier: 4.425A pdb=" N GLU A1059 " --> pdb=" O ILE A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1079 No H-bonds generated for 'chain 'A' and resid 1077 through 1079' Processing helix chain 'A' and resid 1080 through 1086 removed outlier: 3.980A pdb=" N LEU A1086 " --> pdb=" O LYS A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1123 removed outlier: 3.950A pdb=" N ILE A1119 " --> pdb=" O GLU A1115 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP A1120 " --> pdb=" O SER A1116 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A1121 " --> pdb=" O GLU A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1133 Processing helix chain 'A' and resid 1150 through 1166 removed outlier: 3.780A pdb=" N GLN A1155 " --> pdb=" O GLY A1151 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG A1156 " --> pdb=" O GLY A1152 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A1157 " --> pdb=" O GLN A1153 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A1158 " --> pdb=" O LYS A1154 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A1160 " --> pdb=" O ARG A1156 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A1162 " --> pdb=" O ALA A1158 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A1164 " --> pdb=" O ALA A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1240 through 1246 removed outlier: 3.901A pdb=" N LEU A1244 " --> pdb=" O ALA A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1249 No H-bonds generated for 'chain 'A' and resid 1247 through 1249' Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 371 removed outlier: 5.812A pdb=" N PHE A 367 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU A 425 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ASP A 369 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN A 423 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 421 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 443 through 446 removed outlier: 5.627A pdb=" N GLY A 444 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU A 525 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ALA A 572 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ALA A 397 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 574 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL A 399 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL A 573 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 645 through 646 Processing sheet with id=AA4, first strand: chain 'A' and resid 1028 through 1034 removed outlier: 5.864A pdb=" N ARG A1029 " --> pdb=" O PHE A1017 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N PHE A1017 " --> pdb=" O ARG A1029 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A1015 " --> pdb=" O PHE A1031 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU A1033 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ARG A1013 " --> pdb=" O LEU A1033 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1040 through 1041 removed outlier: 7.109A pdb=" N GLY A1089 " --> pdb=" O LEU A1171 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1216 through 1220 removed outlier: 6.657A pdb=" N ILE A1216 " --> pdb=" O GLN A1227 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLN A1227 " --> pdb=" O ILE A1216 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL A1218 " --> pdb=" O VAL A1225 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 642 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1549 1.32 - 1.44: 2513 1.44 - 1.56: 5394 1.56 - 1.69: 1 1.69 - 1.81: 67 Bond restraints: 9524 Sorted by residual: bond pdb=" CA ILE A 195 " pdb=" C ILE A 195 " ideal model delta sigma weight residual 1.520 1.536 -0.016 8.80e-03 1.29e+04 3.27e+00 bond pdb=" C ALA A 668 " pdb=" N PRO A 669 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.30e-02 5.92e+03 2.19e+00 bond pdb=" C ILE A 195 " pdb=" N PRO A 196 " ideal model delta sigma weight residual 1.334 1.345 -0.012 8.40e-03 1.42e+04 1.98e+00 bond pdb=" CB PRO A 56 " pdb=" CG PRO A 56 " ideal model delta sigma weight residual 1.492 1.429 0.063 5.00e-02 4.00e+02 1.59e+00 bond pdb=" N VAL A 605 " pdb=" CA VAL A 605 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.90e-02 2.77e+03 1.56e+00 ... (remaining 9519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 12813 4.23 - 8.47: 74 8.47 - 12.70: 4 12.70 - 16.94: 1 16.94 - 21.17: 6 Bond angle restraints: 12898 Sorted by residual: angle pdb=" C ASN A1126 " pdb=" CA ASN A1126 " pdb=" CB ASN A1126 " ideal model delta sigma weight residual 110.26 89.59 20.67 1.50e+00 4.44e-01 1.90e+02 angle pdb=" N ASN A1126 " pdb=" CA ASN A1126 " pdb=" C ASN A1126 " ideal model delta sigma weight residual 109.59 91.32 18.27 1.47e+00 4.63e-01 1.54e+02 angle pdb=" N ARG A 653 " pdb=" CA ARG A 653 " pdb=" CB ARG A 653 " ideal model delta sigma weight residual 110.39 90.68 19.71 1.59e+00 3.96e-01 1.54e+02 angle pdb=" C PHE A 69 " pdb=" CA PHE A 69 " pdb=" CB PHE A 69 " ideal model delta sigma weight residual 110.70 131.83 -21.13 1.83e+00 2.99e-01 1.33e+02 angle pdb=" N GLY A 652 " pdb=" CA GLY A 652 " pdb=" C GLY A 652 " ideal model delta sigma weight residual 113.18 92.01 21.17 2.37e+00 1.78e-01 7.98e+01 ... (remaining 12893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.44: 5603 26.44 - 52.89: 97 52.89 - 79.33: 13 79.33 - 105.77: 2 105.77 - 132.21: 1 Dihedral angle restraints: 5716 sinusoidal: 2228 harmonic: 3488 Sorted by residual: dihedral pdb=" C ASN A1126 " pdb=" N ASN A1126 " pdb=" CA ASN A1126 " pdb=" CB ASN A1126 " ideal model delta harmonic sigma weight residual -122.60 -90.00 -32.60 0 2.50e+00 1.60e-01 1.70e+02 dihedral pdb=" C PHE A 69 " pdb=" N PHE A 69 " pdb=" CA PHE A 69 " pdb=" CB PHE A 69 " ideal model delta harmonic sigma weight residual -122.60 -151.08 28.48 0 2.50e+00 1.60e-01 1.30e+02 dihedral pdb=" N ALA A1127 " pdb=" C ALA A1127 " pdb=" CA ALA A1127 " pdb=" CB ALA A1127 " ideal model delta harmonic sigma weight residual 122.90 99.33 23.57 0 2.50e+00 1.60e-01 8.89e+01 ... (remaining 5713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 1481 0.208 - 0.417: 7 0.417 - 0.625: 1 0.625 - 0.834: 2 0.834 - 1.042: 1 Chirality restraints: 1492 Sorted by residual: chirality pdb=" CA PHE A 69 " pdb=" N PHE A 69 " pdb=" C PHE A 69 " pdb=" CB PHE A 69 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.71e+01 chirality pdb=" CA ASN A1126 " pdb=" N ASN A1126 " pdb=" C ASN A1126 " pdb=" CB ASN A1126 " both_signs ideal model delta sigma weight residual False 2.51 3.26 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CA ALA A1127 " pdb=" N ALA A1127 " pdb=" C ALA A1127 " pdb=" CB ALA A1127 " both_signs ideal model delta sigma weight residual False 2.48 3.14 -0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 1489 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 681 " -0.072 5.00e-02 4.00e+02 1.09e-01 1.92e+01 pdb=" N PRO A 682 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO A 682 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 682 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 701 " -0.045 5.00e-02 4.00e+02 6.73e-02 7.24e+00 pdb=" N PRO A 702 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 702 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 702 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 195 " 0.042 5.00e-02 4.00e+02 6.28e-02 6.30e+00 pdb=" N PRO A 196 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 196 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 196 " 0.035 5.00e-02 4.00e+02 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 1.00 - 1.78: 2 1.78 - 2.56: 55 2.56 - 3.34: 10734 3.34 - 4.12: 20304 4.12 - 4.90: 38073 Nonbonded interactions: 69168 Sorted by model distance: nonbonded pdb=" O ASN A1126 " pdb=" OD1 ASN A1126 " model vdw 1.004 3.040 nonbonded pdb=" O ASN A1126 " pdb=" CG ASN A1126 " model vdw 1.707 3.270 nonbonded pdb=" C ASN A1126 " pdb=" OD1 ASN A1126 " model vdw 2.081 3.270 nonbonded pdb=" OG SER A 697 " pdb=" O ALA A 744 " model vdw 2.274 3.040 nonbonded pdb=" OE2 GLU A 829 " pdb=" OG SER A 944 " model vdw 2.335 3.040 ... (remaining 69163 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: 1.050 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.870 Find NCS groups from input model: 0.090 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 0.063 9524 Z= 0.299 Angle : 1.036 21.171 12898 Z= 0.592 Chirality : 0.067 1.042 1492 Planarity : 0.007 0.109 1640 Dihedral : 11.185 132.215 3488 Min Nonbonded Distance : 1.004 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.08 % 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: -6.42 (0.15), residues: 1213 helix: -4.87 (0.07), residues: 634 sheet: -3.52 (0.50), residues: 72 loop : -3.31 (0.22), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 933 HIS 0.010 0.002 HIS A 51 PHE 0.026 0.002 PHE A 69 TYR 0.016 0.002 TYR A 730 ARG 0.006 0.001 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8607 (m-30) cc_final: 0.8382 (m-30) REVERT: A 218 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 543 GLN cc_start: 0.9035 (tp-100) cc_final: 0.8467 (tp-100) REVERT: A 708 MET cc_start: 0.8645 (tmm) cc_final: 0.8406 (tmm) REVERT: A 1006 ILE cc_start: 0.8354 (mm) cc_final: 0.8063 (tp) REVERT: A 1026 MET cc_start: 0.6611 (mmm) cc_final: 0.6287 (mmm) REVERT: A 1156 ARG cc_start: 0.8362 (mtt-85) cc_final: 0.7493 (tpp80) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.3212 time to fit residues: 79.4655 Evaluate side-chains 107 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 30.0000 chunk 70 optimal weight: 1.9990 chunk 109 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 168 HIS A 503 GLN A 602 GLN A 680 ASN A 758 ASN ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1041 GLN A1205 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.178479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.129861 restraints weight = 12188.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.128028 restraints weight = 8756.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128849 restraints weight = 9654.051| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9524 Z= 0.167 Angle : 0.610 9.332 12898 Z= 0.333 Chirality : 0.042 0.169 1492 Planarity : 0.005 0.083 1640 Dihedral : 6.827 60.514 1407 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.63 % Allowed : 7.03 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.47 (0.18), residues: 1213 helix: -4.01 (0.11), residues: 640 sheet: -3.04 (0.55), residues: 72 loop : -2.95 (0.24), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 684 HIS 0.004 0.001 HIS A 784 PHE 0.024 0.001 PHE A1130 TYR 0.012 0.001 TYR A 740 ARG 0.005 0.000 ARG A 725 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.920 Fit side-chains REVERT: A 218 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7631 (tm-30) REVERT: A 449 GLU cc_start: 0.7721 (pm20) cc_final: 0.7341 (pm20) REVERT: A 576 GLN cc_start: 0.8207 (pm20) cc_final: 0.7625 (tm-30) REVERT: A 1006 ILE cc_start: 0.8232 (mm) cc_final: 0.7990 (tp) outliers start: 16 outliers final: 6 residues processed: 142 average time/residue: 0.2392 time to fit residues: 47.2466 Evaluate side-chains 104 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1063 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 97 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS A 78 GLN A 483 HIS ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.172046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.125812 restraints weight = 12389.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.121797 restraints weight = 11025.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.122785 restraints weight = 12586.963| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9524 Z= 0.375 Angle : 0.697 14.249 12898 Z= 0.368 Chirality : 0.045 0.146 1492 Planarity : 0.005 0.081 1640 Dihedral : 6.759 54.081 1407 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.24 % Allowed : 9.58 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -4.83 (0.20), residues: 1213 helix: -3.35 (0.15), residues: 643 sheet: -2.94 (0.52), residues: 82 loop : -2.80 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 283 HIS 0.004 0.001 HIS A1128 PHE 0.028 0.002 PHE A 438 TYR 0.021 0.002 TYR A 740 ARG 0.010 0.001 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7630 (tm-30) REVERT: A 604 MET cc_start: 0.3631 (ttt) cc_final: 0.3080 (ptm) REVERT: A 1014 HIS cc_start: 0.7796 (m90) cc_final: 0.7434 (m-70) outliers start: 22 outliers final: 11 residues processed: 116 average time/residue: 0.2261 time to fit residues: 37.4414 Evaluate side-chains 99 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 734 TYR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1074 LYS Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1203 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 GLN ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.174452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126439 restraints weight = 12217.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.122206 restraints weight = 8851.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123412 restraints weight = 10037.164| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9524 Z= 0.242 Angle : 0.602 12.068 12898 Z= 0.320 Chirality : 0.042 0.142 1492 Planarity : 0.004 0.078 1640 Dihedral : 6.310 47.939 1407 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.94 % Allowed : 11.01 % Favored : 87.05 % 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: -4.29 (0.21), residues: 1213 helix: -2.86 (0.17), residues: 639 sheet: -2.77 (0.53), residues: 82 loop : -2.61 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 185 HIS 0.003 0.001 HIS A 784 PHE 0.026 0.001 PHE A1130 TYR 0.017 0.001 TYR A 740 ARG 0.004 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7919 (mttp) cc_final: 0.7630 (pttm) REVERT: A 124 LEU cc_start: 0.9101 (tp) cc_final: 0.8867 (tp) REVERT: A 218 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7588 (tm-30) REVERT: A 543 GLN cc_start: 0.8709 (tp40) cc_final: 0.8494 (tp40) REVERT: A 604 MET cc_start: 0.3639 (ttt) cc_final: 0.3154 (ptm) REVERT: A 1014 HIS cc_start: 0.7685 (m90) cc_final: 0.7305 (m-70) outliers start: 19 outliers final: 14 residues processed: 115 average time/residue: 0.2348 time to fit residues: 37.5439 Evaluate side-chains 103 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1074 LYS Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1203 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 19 optimal weight: 0.0020 chunk 98 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 0.0170 chunk 102 optimal weight: 2.9990 overall best weight: 1.2032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 GLN A 784 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.174219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127417 restraints weight = 12285.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.123730 restraints weight = 11045.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125200 restraints weight = 12225.246| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9524 Z= 0.229 Angle : 0.584 10.810 12898 Z= 0.311 Chirality : 0.042 0.133 1492 Planarity : 0.004 0.074 1640 Dihedral : 6.110 47.765 1407 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.83 % Allowed : 12.74 % Favored : 85.42 % 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: -3.91 (0.22), residues: 1213 helix: -2.54 (0.18), residues: 638 sheet: -2.71 (0.53), residues: 87 loop : -2.42 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 185 HIS 0.002 0.001 HIS A 865 PHE 0.028 0.001 PHE A1130 TYR 0.018 0.001 TYR A 740 ARG 0.005 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7961 (mttp) cc_final: 0.7590 (pttm) REVERT: A 218 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7600 (tm-30) REVERT: A 604 MET cc_start: 0.3477 (ttt) cc_final: 0.3148 (ptm) REVERT: A 1014 HIS cc_start: 0.7509 (m90) cc_final: 0.7193 (m-70) outliers start: 18 outliers final: 15 residues processed: 110 average time/residue: 0.2179 time to fit residues: 33.9915 Evaluate side-chains 100 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 734 TYR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1074 LYS Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1157 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 69 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 48 optimal weight: 0.0270 chunk 103 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 63 optimal weight: 0.0370 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 680 ASN ** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.196976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.146145 restraints weight = 12322.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.144721 restraints weight = 6535.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.147177 restraints weight = 4727.765| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9524 Z= 0.136 Angle : 0.532 10.170 12898 Z= 0.282 Chirality : 0.040 0.134 1492 Planarity : 0.004 0.072 1640 Dihedral : 5.635 44.456 1407 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.73 % Allowed : 12.44 % Favored : 85.83 % 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: -3.48 (0.23), residues: 1213 helix: -2.13 (0.19), residues: 628 sheet: -2.47 (0.54), residues: 87 loop : -2.32 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 185 HIS 0.002 0.000 HIS A 937 PHE 0.023 0.001 PHE A1130 TYR 0.016 0.001 TYR A 740 ARG 0.003 0.000 ARG A 725 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7843 (mttp) cc_final: 0.7636 (pttm) REVERT: A 218 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7599 (tm-30) REVERT: A 576 GLN cc_start: 0.8371 (pm20) cc_final: 0.7748 (tm-30) REVERT: A 604 MET cc_start: 0.3971 (ttt) cc_final: 0.3288 (ptm) REVERT: A 1014 HIS cc_start: 0.8353 (m90) cc_final: 0.7655 (m-70) outliers start: 17 outliers final: 11 residues processed: 116 average time/residue: 0.2152 time to fit residues: 35.0728 Evaluate side-chains 101 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 734 TYR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1074 LYS Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1198 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 chunk 75 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1250 HIS ** 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 = 0.4266 r_free = 0.4266 target = 0.188660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.140227 restraints weight = 12503.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.135484 restraints weight = 8623.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.137061 restraints weight = 7864.067| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9524 Z= 0.322 Angle : 0.620 8.994 12898 Z= 0.327 Chirality : 0.044 0.166 1492 Planarity : 0.004 0.068 1640 Dihedral : 6.057 50.108 1407 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.94 % Allowed : 13.46 % Favored : 84.61 % 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: -3.43 (0.23), residues: 1213 helix: -2.12 (0.19), residues: 631 sheet: -2.30 (0.55), residues: 87 loop : -2.29 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 283 HIS 0.003 0.001 HIS A 865 PHE 0.023 0.002 PHE A 438 TYR 0.019 0.001 TYR A 740 ARG 0.006 0.000 ARG A1007 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7988 (mttp) cc_final: 0.7633 (pttm) REVERT: A 218 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7720 (tm-30) REVERT: A 543 GLN cc_start: 0.8975 (tp40) cc_final: 0.8635 (tp40) REVERT: A 604 MET cc_start: 0.3655 (ttt) cc_final: 0.3138 (ptm) REVERT: A 1014 HIS cc_start: 0.8018 (m90) cc_final: 0.7562 (m-70) outliers start: 19 outliers final: 16 residues processed: 104 average time/residue: 0.2264 time to fit residues: 33.2267 Evaluate side-chains 101 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 734 TYR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 1074 LYS Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1198 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 94 optimal weight: 0.0270 chunk 93 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 680 ASN ** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.191307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.142081 restraints weight = 12585.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.140556 restraints weight = 8690.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.141559 restraints weight = 6459.088| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9524 Z= 0.211 Angle : 0.561 8.454 12898 Z= 0.298 Chirality : 0.042 0.153 1492 Planarity : 0.004 0.070 1640 Dihedral : 5.867 47.346 1407 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.94 % Allowed : 13.56 % Favored : 84.51 % 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: -3.24 (0.23), residues: 1213 helix: -1.94 (0.19), residues: 630 sheet: -2.21 (0.56), residues: 87 loop : -2.25 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 185 HIS 0.002 0.000 HIS A 865 PHE 0.031 0.001 PHE A1130 TYR 0.019 0.001 TYR A 740 ARG 0.004 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7632 (tm-30) REVERT: A 425 LEU cc_start: 0.8519 (pp) cc_final: 0.8186 (pp) REVERT: A 543 GLN cc_start: 0.8808 (tp40) cc_final: 0.8555 (tp40) REVERT: A 576 GLN cc_start: 0.8102 (pm20) cc_final: 0.7606 (tm-30) REVERT: A 604 MET cc_start: 0.3602 (ttt) cc_final: 0.3220 (ptm) REVERT: A 1014 HIS cc_start: 0.7867 (m90) cc_final: 0.7415 (m-70) outliers start: 19 outliers final: 14 residues processed: 103 average time/residue: 0.2414 time to fit residues: 35.0153 Evaluate side-chains 101 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 1074 LYS Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1198 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 7 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 6 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 49 optimal weight: 0.0040 chunk 38 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A1128 HIS ** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.192133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.143289 restraints weight = 12358.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.140244 restraints weight = 8617.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.140871 restraints weight = 6882.368| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9524 Z= 0.192 Angle : 0.561 11.737 12898 Z= 0.298 Chirality : 0.042 0.151 1492 Planarity : 0.004 0.067 1640 Dihedral : 5.742 46.574 1407 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.22 % Allowed : 14.48 % Favored : 84.30 % 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: -3.10 (0.23), residues: 1213 helix: -1.79 (0.20), residues: 630 sheet: -2.14 (0.57), residues: 87 loop : -2.23 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 185 HIS 0.002 0.000 HIS A 865 PHE 0.029 0.001 PHE A1130 TYR 0.018 0.001 TYR A 740 ARG 0.005 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 1.559 Fit side-chains REVERT: A 218 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7641 (tm-30) REVERT: A 425 LEU cc_start: 0.8499 (pp) cc_final: 0.8177 (pp) REVERT: A 543 GLN cc_start: 0.8828 (tp40) cc_final: 0.8558 (tp40) REVERT: A 576 GLN cc_start: 0.8072 (pm20) cc_final: 0.7606 (tm-30) REVERT: A 604 MET cc_start: 0.3647 (ttt) cc_final: 0.3229 (ptm) REVERT: A 1014 HIS cc_start: 0.7898 (m90) cc_final: 0.7420 (m-70) REVERT: A 1026 MET cc_start: 0.6048 (mmt) cc_final: 0.5787 (mmm) REVERT: A 1070 MET cc_start: 0.7920 (tpt) cc_final: 0.7646 (tpp) outliers start: 12 outliers final: 10 residues processed: 99 average time/residue: 0.2539 time to fit residues: 35.9244 Evaluate side-chains 100 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 1074 LYS Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1157 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.0040 chunk 5 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1128 HIS ** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.193249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.144405 restraints weight = 12487.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.141322 restraints weight = 8269.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.141895 restraints weight = 6728.307| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9524 Z= 0.169 Angle : 0.548 11.938 12898 Z= 0.291 Chirality : 0.041 0.171 1492 Planarity : 0.004 0.068 1640 Dihedral : 5.580 46.129 1407 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.22 % Allowed : 14.78 % Favored : 84.00 % 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: -2.94 (0.23), residues: 1213 helix: -1.61 (0.20), residues: 630 sheet: -1.98 (0.58), residues: 87 loop : -2.26 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 283 HIS 0.002 0.000 HIS A 865 PHE 0.029 0.001 PHE A1130 TYR 0.019 0.001 TYR A 740 ARG 0.004 0.000 ARG A1007 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 1.556 Fit side-chains revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7673 (tm-30) REVERT: A 425 LEU cc_start: 0.8474 (pp) cc_final: 0.8159 (pp) REVERT: A 543 GLN cc_start: 0.8850 (tp40) cc_final: 0.8568 (tp40) REVERT: A 576 GLN cc_start: 0.8134 (pm20) cc_final: 0.7680 (tm-30) REVERT: A 1014 HIS cc_start: 0.7941 (m90) cc_final: 0.7447 (m-70) REVERT: A 1026 MET cc_start: 0.5874 (mmt) cc_final: 0.5643 (mmm) REVERT: A 1070 MET cc_start: 0.7866 (tpt) cc_final: 0.7620 (tpp) outliers start: 12 outliers final: 10 residues processed: 102 average time/residue: 0.3138 time to fit residues: 44.7974 Evaluate side-chains 102 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 1074 LYS Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1157 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 109 optimal weight: 8.9990 chunk 44 optimal weight: 0.4980 chunk 82 optimal weight: 4.9990 chunk 67 optimal weight: 0.0270 chunk 29 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.0040 chunk 71 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.4450 ------------------------------------------------------------------------------- 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 = 0.4339 r_free = 0.4339 target = 0.195977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.146539 restraints weight = 12395.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.145062 restraints weight = 7567.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.145817 restraints weight = 6245.616| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 9524 Z= 0.137 Angle : 0.518 11.484 12898 Z= 0.275 Chirality : 0.040 0.170 1492 Planarity : 0.003 0.064 1640 Dihedral : 5.318 44.611 1407 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.33 % Allowed : 14.68 % Favored : 84.00 % 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: -2.68 (0.24), residues: 1213 helix: -1.35 (0.21), residues: 635 sheet: -1.69 (0.64), residues: 77 loop : -2.24 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 283 HIS 0.001 0.000 HIS A 784 PHE 0.028 0.001 PHE A1130 TYR 0.018 0.001 TYR A 740 ARG 0.003 0.000 ARG A 725 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2927.88 seconds wall clock time: 53 minutes 11.79 seconds (3191.79 seconds total)