Starting phenix.real_space_refine on Sat Jul 20 01:10:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wom_37692/07_2024/8wom_37692_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wom_37692/07_2024/8wom_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wom_37692/07_2024/8wom_37692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wom_37692/07_2024/8wom_37692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wom_37692/07_2024/8wom_37692_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wom_37692/07_2024/8wom_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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.62, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.71 Conformation dependent library (CDL) restraints added in 1.7 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: 1.22 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: 3.16 Time building geometry restraints manager: 4.02 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: 89.59 - 98.48: 6 98.48 - 107.38: 278 107.38 - 116.27: 5919 116.27 - 125.16: 6578 125.16 - 134.05: 117 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 2.440 nonbonded pdb=" OE2 GLU A 829 " pdb=" OG SER A 944 " model vdw 2.335 2.440 ... (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: 0.820 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: 0.070 Set scattering table: 0.090 Process input model: 29.410 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.860 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.969 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: 0.2904 time to fit residues: 71.0742 Evaluate side-chains 107 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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: 0.6980 chunk 91 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 30.0000 chunk 70 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS A 168 HIS A 350 GLN A 503 GLN A 602 GLN A 748 GLN A 758 ASN ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1041 GLN A1205 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9524 Z= 0.336 Angle : 0.681 10.064 12898 Z= 0.369 Chirality : 0.045 0.161 1492 Planarity : 0.006 0.091 1640 Dihedral : 7.219 62.964 1407 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.83 % Allowed : 7.65 % Favored : 90.52 % 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: -5.57 (0.18), residues: 1213 helix: -4.06 (0.11), residues: 657 sheet: -3.08 (0.54), residues: 72 loop : -2.97 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 283 HIS 0.005 0.001 HIS A 784 PHE 0.027 0.002 PHE A1130 TYR 0.017 0.002 TYR A 740 ARG 0.005 0.001 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 128 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 0.956 Fit side-chains REVERT: A 218 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7616 (tm-30) REVERT: A 1006 ILE cc_start: 0.8334 (mm) cc_final: 0.7987 (tp) outliers start: 18 outliers final: 7 residues processed: 127 average time/residue: 0.2075 time to fit residues: 37.3006 Evaluate side-chains 97 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1203 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 37 optimal weight: 0.0070 chunk 88 optimal weight: 0.5980 overall best weight: 1.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9524 Z= 0.269 Angle : 0.629 14.012 12898 Z= 0.334 Chirality : 0.043 0.151 1492 Planarity : 0.005 0.083 1640 Dihedral : 6.580 48.685 1407 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.45 % Allowed : 9.68 % Favored : 87.87 % 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: -4.76 (0.20), residues: 1213 helix: -3.30 (0.15), residues: 656 sheet: -2.84 (0.56), residues: 72 loop : -2.75 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 185 HIS 0.003 0.001 HIS A 937 PHE 0.029 0.002 PHE A 438 TYR 0.014 0.001 TYR A 740 ARG 0.004 0.000 ARG A 384 *********************** 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 129 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7601 (tm-30) REVERT: A 457 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8472 (mm) REVERT: A 604 MET cc_start: 0.3965 (ttt) cc_final: 0.3258 (ptm) REVERT: A 1014 HIS cc_start: 0.8180 (m90) cc_final: 0.7658 (m-70) outliers start: 24 outliers final: 14 residues processed: 123 average time/residue: 0.2250 time to fit residues: 38.7994 Evaluate side-chains 107 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 138 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 556 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 1120 ASP 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 108 optimal weight: 5.9990 chunk 82 optimal weight: 0.3980 chunk 57 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 104 optimal weight: 0.3980 chunk 31 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 GLN A 784 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9524 Z= 0.271 Angle : 0.606 11.874 12898 Z= 0.324 Chirality : 0.043 0.138 1492 Planarity : 0.004 0.076 1640 Dihedral : 6.395 49.147 1407 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.65 % Allowed : 10.91 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.21), residues: 1213 helix: -2.90 (0.17), residues: 654 sheet: -2.62 (0.57), residues: 72 loop : -2.56 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 185 HIS 0.003 0.001 HIS A 937 PHE 0.027 0.002 PHE A1130 TYR 0.014 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 126 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 100 time to evaluate : 1.051 Fit side-chains REVERT: A 35 LYS cc_start: 0.7819 (mttp) cc_final: 0.7562 (pttm) REVERT: A 218 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7620 (tm-30) REVERT: A 457 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8508 (mm) REVERT: A 543 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8871 (tp40) REVERT: A 604 MET cc_start: 0.4007 (ttt) cc_final: 0.3331 (ptm) REVERT: A 1014 HIS cc_start: 0.8089 (m90) cc_final: 0.7500 (m-70) outliers start: 26 outliers final: 19 residues processed: 119 average time/residue: 0.2391 time to fit residues: 39.2413 Evaluate side-chains 112 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 212 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 543 GLN 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 959 THR 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 1120 ASP Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1215 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 99 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 680 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9524 Z= 0.131 Angle : 0.539 10.225 12898 Z= 0.287 Chirality : 0.040 0.162 1492 Planarity : 0.004 0.070 1640 Dihedral : 5.802 44.740 1407 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.14 % Allowed : 12.33 % Favored : 85.52 % 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: -3.74 (0.22), residues: 1213 helix: -2.42 (0.18), residues: 641 sheet: -2.44 (0.58), residues: 74 loop : -2.36 (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 0.028 0.001 PHE A1130 TYR 0.012 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 130 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.041 Fit side-chains REVERT: A 35 LYS cc_start: 0.7809 (mttp) cc_final: 0.7584 (pttm) REVERT: A 218 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7606 (tm-30) REVERT: A 543 GLN cc_start: 0.9061 (tp40) cc_final: 0.8822 (tm-30) REVERT: A 604 MET cc_start: 0.3875 (ttt) cc_final: 0.3274 (ptm) REVERT: A 1014 HIS cc_start: 0.8133 (m90) cc_final: 0.7533 (m-70) REVERT: A 1193 ARG cc_start: 0.8051 (mmm-85) cc_final: 0.7808 (mtm180) outliers start: 21 outliers final: 12 residues processed: 125 average time/residue: 0.2306 time to fit residues: 39.8797 Evaluate side-chains 104 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1074 LYS Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1203 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 117 optimal weight: 0.0000 chunk 97 optimal weight: 8.9990 chunk 54 optimal weight: 0.0040 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9524 Z= 0.219 Angle : 0.561 9.751 12898 Z= 0.296 Chirality : 0.042 0.133 1492 Planarity : 0.004 0.067 1640 Dihedral : 5.846 47.797 1407 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.45 % Allowed : 12.44 % Favored : 85.12 % 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: -3.53 (0.23), residues: 1213 helix: -2.19 (0.19), residues: 639 sheet: -2.51 (0.53), residues: 87 loop : -2.30 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 283 HIS 0.002 0.000 HIS A 937 PHE 0.023 0.001 PHE A1130 TYR 0.012 0.001 TYR A 740 ARG 0.005 0.000 ARG A 384 *********************** 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 118 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 1.110 Fit side-chains REVERT: A 35 LYS cc_start: 0.7818 (mttp) cc_final: 0.7590 (pttm) REVERT: A 218 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7702 (tm-30) REVERT: A 543 GLN cc_start: 0.9125 (tp40) cc_final: 0.8727 (tp40) REVERT: A 604 MET cc_start: 0.3929 (ttt) cc_final: 0.3289 (ptm) REVERT: A 1014 HIS cc_start: 0.8057 (m90) cc_final: 0.7478 (m-70) REVERT: A 1193 ARG cc_start: 0.8107 (mmm-85) cc_final: 0.7851 (mtm180) outliers start: 24 outliers final: 19 residues processed: 109 average time/residue: 0.2293 time to fit residues: 35.1565 Evaluate side-chains 108 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 421 SER 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 734 TYR 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 1120 ASP Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1215 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 GLN ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9524 Z= 0.157 Angle : 0.520 8.415 12898 Z= 0.276 Chirality : 0.040 0.134 1492 Planarity : 0.004 0.067 1640 Dihedral : 5.627 46.032 1407 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.45 % Allowed : 13.15 % Favored : 84.40 % 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: -3.29 (0.23), residues: 1213 helix: -1.93 (0.19), residues: 642 sheet: -2.32 (0.54), residues: 87 loop : -2.32 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 185 HIS 0.001 0.000 HIS A 937 PHE 0.024 0.001 PHE A 438 TYR 0.011 0.001 TYR A 740 ARG 0.005 0.000 ARG A 384 *********************** 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 119 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 1.102 Fit side-chains REVERT: A 218 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7690 (tm-30) REVERT: A 384 ARG cc_start: 0.8185 (ttm-80) cc_final: 0.7926 (tpp80) REVERT: A 576 GLN cc_start: 0.8180 (pm20) cc_final: 0.7609 (tm-30) REVERT: A 604 MET cc_start: 0.3810 (ttt) cc_final: 0.3218 (ptm) REVERT: A 1014 HIS cc_start: 0.8057 (m90) cc_final: 0.7438 (m-70) REVERT: A 1193 ARG cc_start: 0.8111 (mmm-85) cc_final: 0.7857 (mtm180) outliers start: 24 outliers final: 20 residues processed: 111 average time/residue: 0.2437 time to fit residues: 37.8863 Evaluate side-chains 109 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 421 SER 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 870 MET Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 991 THR 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 1120 ASP Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1215 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 111 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 chunk 108 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1093 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9524 Z= 0.263 Angle : 0.570 8.153 12898 Z= 0.300 Chirality : 0.042 0.131 1492 Planarity : 0.004 0.067 1640 Dihedral : 5.838 48.953 1407 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.34 % Allowed : 14.37 % Favored : 83.28 % 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: -3.22 (0.23), residues: 1213 helix: -1.89 (0.20), residues: 643 sheet: -2.22 (0.56), residues: 86 loop : -2.28 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 283 HIS 0.002 0.001 HIS A 168 PHE 0.024 0.002 PHE A 438 TYR 0.011 0.001 TYR A 740 ARG 0.003 0.000 ARG A1078 *********************** 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 fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 1.257 Fit side-chains REVERT: A 218 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7607 (tm-30) REVERT: A 543 GLN cc_start: 0.9187 (tp40) cc_final: 0.8640 (tp-100) REVERT: A 576 GLN cc_start: 0.8187 (pm20) cc_final: 0.7615 (tm-30) REVERT: A 604 MET cc_start: 0.3967 (ttt) cc_final: 0.3354 (ptm) REVERT: A 1014 HIS cc_start: 0.8096 (m90) cc_final: 0.7563 (m-70) REVERT: A 1193 ARG cc_start: 0.8182 (mmm-85) cc_final: 0.7899 (mtm180) outliers start: 23 outliers final: 20 residues processed: 103 average time/residue: 0.2405 time to fit residues: 34.2865 Evaluate side-chains 107 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 421 SER 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 709 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1074 LYS Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1215 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 0.0020 chunk 98 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A 543 GLN ** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9524 Z= 0.153 Angle : 0.518 7.652 12898 Z= 0.273 Chirality : 0.040 0.133 1492 Planarity : 0.003 0.067 1640 Dihedral : 5.550 45.761 1407 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.24 % Allowed : 14.68 % Favored : 83.08 % 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: -2.93 (0.24), residues: 1213 helix: -1.63 (0.20), residues: 632 sheet: -1.89 (0.59), residues: 84 loop : -2.22 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 185 HIS 0.001 0.000 HIS A 937 PHE 0.030 0.001 PHE A1130 TYR 0.011 0.001 TYR A 740 ARG 0.005 0.000 ARG A1078 *********************** 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 115 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 1.102 Fit side-chains REVERT: A 218 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7717 (tm-30) REVERT: A 576 GLN cc_start: 0.8151 (pm20) cc_final: 0.7626 (tm-30) REVERT: A 604 MET cc_start: 0.3936 (ttt) cc_final: 0.3361 (ptm) REVERT: A 1014 HIS cc_start: 0.8095 (m90) cc_final: 0.7515 (m-70) REVERT: A 1026 MET cc_start: 0.6123 (mmt) cc_final: 0.5880 (mmm) REVERT: A 1070 MET cc_start: 0.8331 (tpp) cc_final: 0.7825 (tpp) REVERT: A 1193 ARG cc_start: 0.8176 (mmm-85) cc_final: 0.7970 (mtm180) outliers start: 22 outliers final: 19 residues processed: 107 average time/residue: 0.2412 time to fit residues: 35.4510 Evaluate side-chains 106 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1215 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 0.0470 chunk 58 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9524 Z= 0.221 Angle : 0.561 12.752 12898 Z= 0.295 Chirality : 0.042 0.187 1492 Planarity : 0.004 0.066 1640 Dihedral : 5.647 47.775 1407 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.45 % Allowed : 14.58 % Favored : 82.98 % 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: -2.85 (0.24), residues: 1213 helix: -1.57 (0.20), residues: 630 sheet: -1.78 (0.60), residues: 84 loop : -2.18 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 283 HIS 0.001 0.000 HIS A 168 PHE 0.031 0.001 PHE A1130 TYR 0.012 0.001 TYR A 740 ARG 0.004 0.000 ARG A1078 ********************** 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 110 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 1.055 Fit side-chains REVERT: A 218 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7732 (tm-30) REVERT: A 543 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8802 (tp40) REVERT: A 576 GLN cc_start: 0.8170 (pm20) cc_final: 0.7637 (tm-30) REVERT: A 604 MET cc_start: 0.3967 (ttt) cc_final: 0.3384 (ptm) REVERT: A 1014 HIS cc_start: 0.8149 (m90) cc_final: 0.7575 (m-70) REVERT: A 1026 MET cc_start: 0.6093 (mmt) cc_final: 0.5843 (mmm) REVERT: A 1070 MET cc_start: 0.8373 (tpp) cc_final: 0.7847 (tpp) REVERT: A 1193 ARG cc_start: 0.8186 (mmm-85) cc_final: 0.7971 (mtm180) outliers start: 24 outliers final: 22 residues processed: 103 average time/residue: 0.2294 time to fit residues: 33.1345 Evaluate side-chains 107 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 734 TYR Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1063 ASP Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1215 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.6980 chunk 14 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4303 r_free = 0.4303 target = 0.192862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.142964 restraints weight = 12261.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.140896 restraints weight = 8076.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.142489 restraints weight = 6189.708| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9524 Z= 0.174 Angle : 0.539 11.753 12898 Z= 0.283 Chirality : 0.041 0.180 1492 Planarity : 0.004 0.068 1640 Dihedral : 5.544 46.716 1407 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.24 % Allowed : 14.88 % Favored : 82.87 % 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: -2.71 (0.24), residues: 1213 helix: -1.43 (0.21), residues: 636 sheet: -1.41 (0.66), residues: 77 loop : -2.22 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 185 HIS 0.001 0.000 HIS A 168 PHE 0.032 0.001 PHE A1130 TYR 0.012 0.001 TYR A 740 ARG 0.005 0.000 ARG A1243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1918.48 seconds wall clock time: 35 minutes 2.45 seconds (2102.45 seconds total)