Starting phenix.real_space_refine on Wed Apr 30 22:19:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iz7_35834/04_2025/8iz7_35834_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iz7_35834/04_2025/8iz7_35834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iz7_35834/04_2025/8iz7_35834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iz7_35834/04_2025/8iz7_35834.map" model { file = "/net/cci-nas-00/data/ceres_data/8iz7_35834/04_2025/8iz7_35834_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iz7_35834/04_2025/8iz7_35834_trim.cif" } resolution = 3.8 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= 0.043 sd= 0.125 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 44 5.16 5 C 6385 2.51 5 N 1650 2.21 5 O 1750 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9830 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1229, 9805 Classifications: {'peptide': 1229} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 1190} Chain breaks: 2 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'SUZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.11, per 1000 atoms: 0.62 Number of scatterers: 9830 At special positions: 0 Unit cell: (76.54, 113.52, 161.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 F 1 9.00 O 1750 8.00 N 1650 7.00 C 6385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.1 seconds 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 4 sheets defined 60.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 17 through 23 Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 27 through 37 removed outlier: 3.686A pdb=" N LYS A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 44 removed outlier: 4.049A pdb=" N MET A 44 " --> pdb=" O GLU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 73 removed outlier: 4.177A pdb=" N GLU A 59 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 68 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG A 70 " --> pdb=" O LYS A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 removed outlier: 3.502A pdb=" N CYS A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 88 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 97 through 102 removed outlier: 3.767A pdb=" N ILE A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 102' Processing helix chain 'A' and resid 107 through 118 removed outlier: 3.989A pdb=" N ILE A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.611A pdb=" N ASN A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR A 123 " --> pdb=" O PHE A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 119 through 123' Processing helix chain 'A' and resid 127 through 145 removed outlier: 4.330A pdb=" N ALA A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR A 137 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'A' and resid 152 through 177 removed outlier: 3.829A pdb=" N ALA A 162 " --> pdb=" O HIS A 158 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET A 164 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR A 175 " --> pdb=" O CYS A 171 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 176 " --> pdb=" O HIS A 172 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS A 177 " --> pdb=" O MET A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 Processing helix chain 'A' and resid 190 through 195 removed outlier: 4.407A pdb=" N ILE A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 190 through 195' Processing helix chain 'A' and resid 204 through 212 removed outlier: 4.119A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 217 through 231 removed outlier: 3.861A pdb=" N GLN A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 237 through 261 removed outlier: 3.733A pdb=" N MET A 241 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 4.021A pdb=" N SER A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 255 " --> pdb=" O GLN A 251 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 257 " --> pdb=" O CYS A 253 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.882A pdb=" N THR A 267 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 removed outlier: 3.804A pdb=" N THR A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 291 through 303 removed outlier: 3.928A pdb=" N ASN A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 299 " --> pdb=" O PHE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 322 through 327 removed outlier: 3.674A pdb=" N SER A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.795A pdb=" N THR A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.938A pdb=" N ALA A 360 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 356 through 361' Processing helix chain 'A' and resid 370 through 375 Processing helix chain 'A' and resid 382 through 391 removed outlier: 4.552A pdb=" N THR A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 460 Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 500 through 512 Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 522 through 526 removed outlier: 3.589A pdb=" N LEU A 525 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR A 526 " --> pdb=" O GLY A 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 522 through 526' Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.527A pdb=" N GLY A 532 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR A 533 " --> pdb=" O ASP A 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 529 through 533' Processing helix chain 'A' and resid 536 through 551 Processing helix chain 'A' and resid 566 through 578 Processing helix chain 'A' and resid 580 through 584 removed outlier: 3.753A pdb=" N HIS A 583 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU A 584 " --> pdb=" O ILE A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 584' Processing helix chain 'A' and resid 593 through 597 removed outlier: 3.881A pdb=" N TYR A 596 " --> pdb=" O GLN A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 623 Processing helix chain 'A' and resid 626 through 632 removed outlier: 3.676A pdb=" N LEU A 630 " --> pdb=" O ASP A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 707 removed outlier: 3.944A pdb=" N TYR A 701 " --> pdb=" O GLY A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 730 removed outlier: 4.047A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ALA A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 730 " --> pdb=" O VAL A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 743 removed outlier: 3.771A pdb=" N LYS A 741 " --> pdb=" O TYR A 737 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 773 removed outlier: 3.533A pdb=" N TYR A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLY A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 removed outlier: 3.504A pdb=" N ILE A 780 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 776 through 781' Processing helix chain 'A' and resid 785 through 798 removed outlier: 3.628A pdb=" N SER A 794 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS A 798 " --> pdb=" O SER A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 803 removed outlier: 3.623A pdb=" N GLU A 803 " --> pdb=" O ASN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 removed outlier: 3.780A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 815 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 816 " --> pdb=" O PHE A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 856 removed outlier: 3.892A pdb=" N ASP A 842 " --> pdb=" O LEU A 838 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 843 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR A 846 " --> pdb=" O ASP A 842 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 848 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN A 849 " --> pdb=" O GLN A 845 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL A 853 " --> pdb=" O GLN A 849 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 854 " --> pdb=" O VAL A 850 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 855 " --> pdb=" O VAL A 851 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 867 No H-bonds generated for 'chain 'A' and resid 865 through 867' Processing helix chain 'A' and resid 868 through 883 removed outlier: 3.513A pdb=" N ARG A 880 " --> pdb=" O ILE A 876 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 896 removed outlier: 3.615A pdb=" N VAL A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 905 Processing helix chain 'A' and resid 924 through 936 removed outlier: 3.677A pdb=" N HIS A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 943 removed outlier: 3.868A pdb=" N PHE A 941 " --> pdb=" O ALA A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 949 removed outlier: 3.809A pdb=" N PHE A 948 " --> pdb=" O THR A 944 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 949 " --> pdb=" O SER A 945 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 944 through 949' Processing helix chain 'A' and resid 960 through 969 removed outlier: 3.547A pdb=" N ALA A 964 " --> pdb=" O VAL A 960 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY A 966 " --> pdb=" O ILE A 962 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 969 " --> pdb=" O PHE A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 974 removed outlier: 3.638A pdb=" N LEU A 974 " --> pdb=" O ALA A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 986 removed outlier: 3.537A pdb=" N LEU A 983 " --> pdb=" O VAL A 979 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 986 " --> pdb=" O ALA A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1006 removed outlier: 3.610A pdb=" N ARG A 998 " --> pdb=" O GLN A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1016 Processing helix chain 'A' and resid 1080 through 1089 removed outlier: 3.608A pdb=" N LEU A1084 " --> pdb=" O GLY A1080 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1115 Processing helix chain 'A' and resid 1130 through 1136 Processing helix chain 'A' and resid 1142 through 1153 Processing helix chain 'A' and resid 1156 through 1161 removed outlier: 3.978A pdb=" N ASP A1161 " --> pdb=" O GLU A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1175 removed outlier: 3.618A pdb=" N GLY A1174 " --> pdb=" O ALA A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1194 removed outlier: 3.507A pdb=" N LYS A1194 " --> pdb=" O ALA A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1222 Processing helix chain 'A' and resid 1257 through 1263 removed outlier: 3.587A pdb=" N GLN A1263 " --> pdb=" O TYR A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1275 removed outlier: 3.867A pdb=" N LYS A1271 " --> pdb=" O SER A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1297 Processing sheet with id=AA1, first strand: chain 'A' and resid 431 through 435 removed outlier: 7.265A pdb=" N PHE A 433 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLN A 413 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL A 435 " --> pdb=" O HIS A 411 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N HIS A 411 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL A 412 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N SER A 470 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ASP A 414 " --> pdb=" O LEU A 468 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU A 468 " --> pdb=" O ASP A 414 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.548A pdb=" N TYR A 556 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL A 590 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A 558 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN A 613 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS A 607 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N MET A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1061 through 1065 removed outlier: 5.872A pdb=" N LEU A1061 " --> pdb=" O ASN A1045 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A1045 " --> pdb=" O LEU A1061 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE A1043 " --> pdb=" O TRP A1099 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N TRP A1099 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN A1045 " --> pdb=" O LYS A1097 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A1097 " --> pdb=" O ASN A1045 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1118 through 1120 removed outlier: 3.578A pdb=" N VAL A1071 " --> pdb=" O VAL A1228 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A1230 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) 364 hydrogen bonds defined for protein. 1053 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: 3.24 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3107 1.34 - 1.46: 2339 1.46 - 1.58: 4524 1.58 - 1.70: 2 1.70 - 1.82: 70 Bond restraints: 10042 Sorted by residual: bond pdb=" C2 SUZ A1401 " pdb=" S SUZ A1401 " ideal model delta sigma weight residual 1.792 1.562 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C1 SUZ A1401 " pdb=" S SUZ A1401 " ideal model delta sigma weight residual 1.808 1.654 0.154 2.00e-02 2.50e+03 5.94e+01 bond pdb=" C6 SUZ A1401 " pdb=" C7 SUZ A1401 " ideal model delta sigma weight residual 1.344 1.489 -0.145 2.00e-02 2.50e+03 5.29e+01 bond pdb=" C10 SUZ A1401 " pdb=" C8 SUZ A1401 " ideal model delta sigma weight residual 1.353 1.487 -0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" O1 SUZ A1401 " pdb=" S SUZ A1401 " ideal model delta sigma weight residual 1.507 1.631 -0.124 2.00e-02 2.50e+03 3.84e+01 ... (remaining 10037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 13450 2.82 - 5.64: 148 5.64 - 8.46: 9 8.46 - 11.28: 2 11.28 - 14.11: 1 Bond angle restraints: 13610 Sorted by residual: angle pdb=" N ILE A 245 " pdb=" CA ILE A 245 " pdb=" C ILE A 245 " ideal model delta sigma weight residual 113.71 105.79 7.92 9.50e-01 1.11e+00 6.95e+01 angle pdb=" N ALA A 724 " pdb=" CA ALA A 724 " pdb=" C ALA A 724 " ideal model delta sigma weight residual 114.75 106.78 7.97 1.26e+00 6.30e-01 4.00e+01 angle pdb=" N TYR A 881 " pdb=" CA TYR A 881 " pdb=" C TYR A 881 " ideal model delta sigma weight residual 114.75 107.03 7.72 1.26e+00 6.30e-01 3.76e+01 angle pdb=" C1 SUZ A1401 " pdb=" S SUZ A1401 " pdb=" C2 SUZ A1401 " ideal model delta sigma weight residual 96.79 110.90 -14.11 3.00e+00 1.11e-01 2.21e+01 angle pdb=" N ARG A 312 " pdb=" CA ARG A 312 " pdb=" C ARG A 312 " ideal model delta sigma weight residual 114.09 106.82 7.27 1.55e+00 4.16e-01 2.20e+01 ... (remaining 13605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.47: 5220 15.47 - 30.94: 586 30.94 - 46.41: 154 46.41 - 61.88: 13 61.88 - 77.35: 11 Dihedral angle restraints: 5984 sinusoidal: 2397 harmonic: 3587 Sorted by residual: dihedral pdb=" CA PHE A 369 " pdb=" C PHE A 369 " pdb=" N PRO A 370 " pdb=" CA PRO A 370 " ideal model delta harmonic sigma weight residual 180.00 156.87 23.13 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA SER A 182 " pdb=" C SER A 182 " pdb=" N ASN A 183 " pdb=" CA ASN A 183 " ideal model delta harmonic sigma weight residual 180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ALA A 723 " pdb=" C ALA A 723 " pdb=" N ALA A 724 " pdb=" CA ALA A 724 " ideal model delta harmonic sigma weight residual 180.00 161.52 18.48 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 5981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 873 0.025 - 0.049: 442 0.049 - 0.074: 147 0.074 - 0.099: 69 0.099 - 0.123: 43 Chirality restraints: 1574 Sorted by residual: chirality pdb=" CA ILE A 245 " pdb=" N ILE A 245 " pdb=" C ILE A 245 " pdb=" CB ILE A 245 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ILE A1073 " pdb=" N ILE A1073 " pdb=" C ILE A1073 " pdb=" CB ILE A1073 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA ILE A1200 " pdb=" N ILE A1200 " pdb=" C ILE A1200 " pdb=" CB ILE A1200 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 ... (remaining 1571 not shown) Planarity restraints: 1690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 SUZ A1401 " -0.021 2.00e-02 2.50e+03 4.10e-02 3.37e+01 pdb=" C2 SUZ A1401 " 0.001 2.00e-02 2.50e+03 pdb=" C20 SUZ A1401 " -0.009 2.00e-02 2.50e+03 pdb=" C3 SUZ A1401 " -0.003 2.00e-02 2.50e+03 pdb=" C4 SUZ A1401 " -0.032 2.00e-02 2.50e+03 pdb=" C5 SUZ A1401 " -0.059 2.00e-02 2.50e+03 pdb=" C6 SUZ A1401 " 0.082 2.00e-02 2.50e+03 pdb=" S SUZ A1401 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 SUZ A1401 " -0.001 2.00e-02 2.50e+03 2.43e-02 1.92e+01 pdb=" C11 SUZ A1401 " -0.010 2.00e-02 2.50e+03 pdb=" C13 SUZ A1401 " -0.001 2.00e-02 2.50e+03 pdb=" C14 SUZ A1401 " -0.012 2.00e-02 2.50e+03 pdb=" C15 SUZ A1401 " -0.005 2.00e-02 2.50e+03 pdb=" C16 SUZ A1401 " 0.019 2.00e-02 2.50e+03 pdb=" C17 SUZ A1401 " 0.034 2.00e-02 2.50e+03 pdb=" C18 SUZ A1401 " 0.000 2.00e-02 2.50e+03 pdb=" C6 SUZ A1401 " -0.065 2.00e-02 2.50e+03 pdb=" C7 SUZ A1401 " 0.024 2.00e-02 2.50e+03 pdb=" C8 SUZ A1401 " 0.017 2.00e-02 2.50e+03 pdb=" C9 SUZ A1401 " 0.020 2.00e-02 2.50e+03 pdb=" F SUZ A1401 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 369 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO A 370 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.022 5.00e-02 4.00e+02 ... (remaining 1687 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1281 2.76 - 3.29: 9109 3.29 - 3.83: 14886 3.83 - 4.36: 16772 4.36 - 4.90: 29234 Nonbonded interactions: 71282 Sorted by model distance: nonbonded pdb=" NH1 ARG A 998 " pdb=" O3 SUZ A1401 " model vdw 2.220 3.120 nonbonded pdb=" OD1 ASP A1208 " pdb=" OG1 THR A1211 " model vdw 2.279 3.040 nonbonded pdb=" O LEU A 940 " pdb=" OG1 THR A 944 " model vdw 2.281 3.040 nonbonded pdb=" O LYS A1070 " pdb=" OG SER A1241 " model vdw 2.296 3.040 nonbonded pdb=" OG SER A 479 " pdb=" O GLN A 481 " model vdw 2.317 3.040 ... (remaining 71277 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: 1.120 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: 0.110 Process input model: 26.020 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 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 : 0.004 0.230 10042 Z= 0.240 Angle : 0.767 14.106 13610 Z= 0.508 Chirality : 0.038 0.123 1574 Planarity : 0.003 0.041 1690 Dihedral : 13.687 77.350 3662 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -4.30 (0.19), residues: 1223 helix: -2.97 (0.15), residues: 697 sheet: -0.99 (0.50), residues: 80 loop : -2.70 (0.24), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 711 HIS 0.003 0.001 HIS A1111 PHE 0.003 0.000 PHE A 418 TYR 0.003 0.000 TYR A1259 ARG 0.001 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.23771 ( 364) hydrogen bonds : angle 6.98247 ( 1053) covalent geometry : bond 0.00445 (10042) covalent geometry : angle 0.76743 (13610) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.6695 (mtm) cc_final: 0.5593 (mtp) REVERT: A 89 TRP cc_start: 0.6655 (p-90) cc_final: 0.5941 (t60) REVERT: A 98 PHE cc_start: 0.7342 (t80) cc_final: 0.6458 (m-10) REVERT: A 562 LEU cc_start: 0.7593 (mm) cc_final: 0.7227 (tt) REVERT: A 744 MET cc_start: 0.8166 (tmm) cc_final: 0.7897 (tpp) REVERT: A 763 TRP cc_start: 0.7548 (t-100) cc_final: 0.6872 (t60) REVERT: A 828 ASP cc_start: 0.7947 (p0) cc_final: 0.7717 (t70) REVERT: A 923 CYS cc_start: 0.7428 (m) cc_final: 0.6746 (m) REVERT: A 975 ASP cc_start: 0.6140 (p0) cc_final: 0.5691 (t0) REVERT: A 1026 GLU cc_start: 0.7713 (pm20) cc_final: 0.7463 (pp20) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2634 time to fit residues: 67.0793 Evaluate side-chains 87 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 0.0030 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 0.3980 chunk 110 optimal weight: 8.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 934 HIS A1141 HIS A1183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.150695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.119931 restraints weight = 22804.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.117139 restraints weight = 25098.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.118402 restraints weight = 22863.534| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10042 Z= 0.132 Angle : 0.637 10.827 13610 Z= 0.313 Chirality : 0.041 0.238 1574 Planarity : 0.005 0.070 1690 Dihedral : 5.058 87.156 1330 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.78 % Allowed : 11.68 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -2.92 (0.21), residues: 1223 helix: -1.91 (0.18), residues: 675 sheet: -0.08 (0.56), residues: 80 loop : -2.08 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 912 HIS 0.006 0.001 HIS A 172 PHE 0.046 0.001 PHE A 369 TYR 0.019 0.002 TYR A 768 ARG 0.004 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 364) hydrogen bonds : angle 4.55307 ( 1053) covalent geometry : bond 0.00291 (10042) covalent geometry : angle 0.63748 (13610) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7795 (t80) REVERT: A 556 TYR cc_start: 0.6755 (m-80) cc_final: 0.6386 (m-80) REVERT: A 1195 ASN cc_start: 0.5893 (m-40) cc_final: 0.5279 (m-40) outliers start: 19 outliers final: 11 residues processed: 119 average time/residue: 0.2231 time to fit residues: 38.0312 Evaluate side-chains 89 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1261 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 2 optimal weight: 0.0670 chunk 22 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 34 optimal weight: 0.0070 chunk 4 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 89 optimal weight: 0.0470 chunk 111 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.0238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1141 HIS A1181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.138068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.105807 restraints weight = 22207.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.102626 restraints weight = 18127.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.103633 restraints weight = 19205.425| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10042 Z= 0.108 Angle : 0.572 9.976 13610 Z= 0.285 Chirality : 0.039 0.193 1574 Planarity : 0.004 0.054 1690 Dihedral : 4.994 89.323 1330 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.24 % Allowed : 13.36 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.23), residues: 1223 helix: -1.44 (0.19), residues: 697 sheet: 0.20 (0.56), residues: 80 loop : -1.70 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 230 HIS 0.004 0.001 HIS A 572 PHE 0.034 0.001 PHE A 369 TYR 0.017 0.001 TYR A 550 ARG 0.003 0.000 ARG A1234 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 364) hydrogen bonds : angle 4.24336 ( 1053) covalent geometry : bond 0.00232 (10042) covalent geometry : angle 0.57175 (13610) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.7893 (t80) REVERT: A 811 LEU cc_start: 0.8512 (tp) cc_final: 0.8260 (mp) REVERT: A 1048 PHE cc_start: 0.8273 (t80) cc_final: 0.8036 (t80) REVERT: A 1195 ASN cc_start: 0.5760 (m-40) cc_final: 0.5048 (m-40) outliers start: 24 outliers final: 13 residues processed: 99 average time/residue: 0.2025 time to fit residues: 29.7928 Evaluate side-chains 85 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1200 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 94 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 153 HIS A 518 GLN A1141 HIS A1151 GLN A1181 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.125926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.093697 restraints weight = 22914.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.090916 restraints weight = 19073.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.091854 restraints weight = 22252.983| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10042 Z= 0.199 Angle : 0.724 10.550 13610 Z= 0.369 Chirality : 0.046 0.192 1574 Planarity : 0.005 0.062 1690 Dihedral : 5.748 78.658 1330 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.11 % Favored : 92.80 % Rotamer: Outliers : 2.90 % Allowed : 15.23 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -2.46 (0.23), residues: 1223 helix: -1.56 (0.19), residues: 708 sheet: 0.15 (0.56), residues: 80 loop : -1.85 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 230 HIS 0.007 0.001 HIS A 903 PHE 0.028 0.002 PHE A 369 TYR 0.026 0.002 TYR A 556 ARG 0.004 0.001 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.05977 ( 364) hydrogen bonds : angle 4.75295 ( 1053) covalent geometry : bond 0.00470 (10042) covalent geometry : angle 0.72405 (13610) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7636 (mtt90) cc_final: 0.7368 (mtp85) REVERT: A 207 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8059 (mt0) REVERT: A 214 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.7907 (t80) REVERT: A 1065 ILE cc_start: 0.7596 (mm) cc_final: 0.7367 (mm) REVERT: A 1093 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6835 (mt-10) REVERT: A 1166 MET cc_start: 0.2783 (pmm) cc_final: 0.0877 (mtm) REVERT: A 1259 TYR cc_start: 0.6577 (t80) cc_final: 0.6347 (t80) outliers start: 31 outliers final: 15 residues processed: 100 average time/residue: 0.1895 time to fit residues: 28.9406 Evaluate side-chains 77 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1093 GLU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1200 ILE Chi-restraints excluded: chain A residue 1237 THR Chi-restraints excluded: chain A residue 1261 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 98 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 78 optimal weight: 0.0870 chunk 3 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.127605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.095210 restraints weight = 23067.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.091963 restraints weight = 19772.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.093068 restraints weight = 19138.328| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10042 Z= 0.119 Angle : 0.596 10.333 13610 Z= 0.297 Chirality : 0.040 0.152 1574 Planarity : 0.004 0.060 1690 Dihedral : 5.212 76.939 1330 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.87 % Allowed : 17.29 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -2.24 (0.23), residues: 1223 helix: -1.35 (0.19), residues: 720 sheet: 0.20 (0.56), residues: 80 loop : -1.80 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 711 HIS 0.004 0.001 HIS A 903 PHE 0.023 0.001 PHE A 369 TYR 0.018 0.001 TYR A 550 ARG 0.003 0.000 ARG A 824 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 364) hydrogen bonds : angle 4.37919 ( 1053) covalent geometry : bond 0.00271 (10042) covalent geometry : angle 0.59551 (13610) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7652 (mtt90) cc_final: 0.7424 (mtp85) REVERT: A 164 MET cc_start: 0.7184 (ttp) cc_final: 0.6912 (ttp) REVERT: A 207 GLN cc_start: 0.8319 (mm-40) cc_final: 0.7876 (mt0) REVERT: A 214 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.7927 (t80) REVERT: A 409 MET cc_start: 0.7379 (pmm) cc_final: 0.5343 (mtp) REVERT: A 820 ARG cc_start: 0.7377 (tpt170) cc_final: 0.6928 (tpm170) REVERT: A 1166 MET cc_start: 0.3141 (pmm) cc_final: 0.1200 (mtm) outliers start: 20 outliers final: 14 residues processed: 81 average time/residue: 0.1849 time to fit residues: 23.0605 Evaluate side-chains 75 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 985 TYR Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1261 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 113 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 61 optimal weight: 0.0170 chunk 53 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1037 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.128033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.095501 restraints weight = 23157.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.092911 restraints weight = 19030.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.093715 restraints weight = 18861.525| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.6305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10042 Z= 0.100 Angle : 0.560 8.305 13610 Z= 0.278 Chirality : 0.040 0.155 1574 Planarity : 0.004 0.059 1690 Dihedral : 4.885 72.431 1330 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.96 % Allowed : 17.76 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.24), residues: 1223 helix: -1.07 (0.20), residues: 704 sheet: 0.40 (0.57), residues: 80 loop : -1.60 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 711 HIS 0.003 0.001 HIS A 903 PHE 0.020 0.001 PHE A 143 TYR 0.023 0.001 TYR A1259 ARG 0.002 0.000 ARG A 824 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 364) hydrogen bonds : angle 4.23536 ( 1053) covalent geometry : bond 0.00225 (10042) covalent geometry : angle 0.56004 (13610) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.7177 (ttp) cc_final: 0.6907 (ttp) REVERT: A 207 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7991 (mt0) REVERT: A 214 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.7938 (t80) REVERT: A 1065 ILE cc_start: 0.7422 (mm) cc_final: 0.6947 (mp) REVERT: A 1166 MET cc_start: 0.3461 (pmm) cc_final: 0.1564 (mtm) outliers start: 21 outliers final: 12 residues processed: 77 average time/residue: 0.1840 time to fit residues: 22.2017 Evaluate side-chains 69 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 985 TYR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1200 ILE Chi-restraints excluded: chain A residue 1261 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 78 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1233 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.127497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.094731 restraints weight = 23297.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.091820 restraints weight = 17767.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.092625 restraints weight = 18822.027| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.6562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10042 Z= 0.112 Angle : 0.571 8.676 13610 Z= 0.283 Chirality : 0.040 0.146 1574 Planarity : 0.004 0.059 1690 Dihedral : 4.809 68.338 1330 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.96 % Allowed : 18.04 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.24), residues: 1223 helix: -1.00 (0.20), residues: 714 sheet: 0.36 (0.57), residues: 80 loop : -1.53 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 711 HIS 0.010 0.001 HIS A1233 PHE 0.018 0.001 PHE A 369 TYR 0.012 0.001 TYR A 556 ARG 0.002 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 364) hydrogen bonds : angle 4.24817 ( 1053) covalent geometry : bond 0.00256 (10042) covalent geometry : angle 0.57061 (13610) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.7249 (ttp) cc_final: 0.6980 (ttp) REVERT: A 207 GLN cc_start: 0.8356 (mm-40) cc_final: 0.7985 (mt0) REVERT: A 214 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7940 (t80) REVERT: A 409 MET cc_start: 0.7328 (pmm) cc_final: 0.5293 (mtp) REVERT: A 1166 MET cc_start: 0.3723 (pmm) cc_final: 0.1921 (mtm) REVERT: A 1259 TYR cc_start: 0.6085 (t80) cc_final: 0.5762 (t80) outliers start: 21 outliers final: 15 residues processed: 73 average time/residue: 0.1999 time to fit residues: 22.5943 Evaluate side-chains 71 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 985 TYR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1200 ILE Chi-restraints excluded: chain A residue 1237 THR Chi-restraints excluded: chain A residue 1261 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 92 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 18 optimal weight: 0.1980 chunk 46 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 107 optimal weight: 0.0040 chunk 23 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 59 optimal weight: 30.0000 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.130046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.097777 restraints weight = 23327.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.095170 restraints weight = 19767.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.096150 restraints weight = 22643.425| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.6581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10042 Z= 0.085 Angle : 0.541 7.485 13610 Z= 0.266 Chirality : 0.039 0.148 1574 Planarity : 0.004 0.058 1690 Dihedral : 4.529 62.741 1330 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.50 % Allowed : 18.97 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.24), residues: 1223 helix: -0.74 (0.20), residues: 712 sheet: 0.41 (0.58), residues: 79 loop : -1.36 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.003 0.001 HIS A 572 PHE 0.016 0.001 PHE A 143 TYR 0.028 0.001 TYR A 550 ARG 0.002 0.000 ARG A 820 Details of bonding type rmsd hydrogen bonds : bond 0.02558 ( 364) hydrogen bonds : angle 4.04311 ( 1053) covalent geometry : bond 0.00181 (10042) covalent geometry : angle 0.54139 (13610) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.7119 (ttp) cc_final: 0.6863 (ttp) REVERT: A 207 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7837 (mt0) REVERT: A 214 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.7988 (t80) REVERT: A 374 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8643 (tm-30) REVERT: A 409 MET cc_start: 0.7451 (pmm) cc_final: 0.5568 (mtp) REVERT: A 1166 MET cc_start: 0.4030 (pmm) cc_final: 0.2201 (mtm) REVERT: A 1259 TYR cc_start: 0.6182 (t80) cc_final: 0.5904 (t80) outliers start: 16 outliers final: 9 residues processed: 71 average time/residue: 0.1827 time to fit residues: 20.6406 Evaluate side-chains 66 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 1028 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1200 ILE Chi-restraints excluded: chain A residue 1261 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.125656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.093799 restraints weight = 23123.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.090669 restraints weight = 21092.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.091525 restraints weight = 21674.073| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.7061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10042 Z= 0.161 Angle : 0.630 8.295 13610 Z= 0.318 Chirality : 0.043 0.150 1574 Planarity : 0.004 0.057 1690 Dihedral : 4.868 55.541 1330 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 1.59 % Allowed : 19.35 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.24), residues: 1223 helix: -0.93 (0.20), residues: 721 sheet: 0.43 (0.58), residues: 79 loop : -1.45 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1147 HIS 0.006 0.001 HIS A 903 PHE 0.062 0.002 PHE A 369 TYR 0.014 0.001 TYR A 339 ARG 0.003 0.000 ARG A 824 Details of bonding type rmsd hydrogen bonds : bond 0.04765 ( 364) hydrogen bonds : angle 4.40660 ( 1053) covalent geometry : bond 0.00381 (10042) covalent geometry : angle 0.62976 (13610) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 1.253 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7643 (mtt90) cc_final: 0.7399 (mtp85) REVERT: A 207 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8147 (mt0) REVERT: A 214 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.7935 (t80) REVERT: A 374 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8544 (tm-30) REVERT: A 1166 MET cc_start: 0.4215 (pmm) cc_final: 0.2612 (mtm) REVERT: A 1259 TYR cc_start: 0.6225 (t80) cc_final: 0.5863 (t80) outliers start: 17 outliers final: 12 residues processed: 68 average time/residue: 0.2381 time to fit residues: 25.7631 Evaluate side-chains 64 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1237 THR Chi-restraints excluded: chain A residue 1261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 78 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 90 optimal weight: 0.0970 chunk 20 optimal weight: 1.9990 chunk 93 optimal weight: 0.1980 chunk 83 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 98 optimal weight: 0.0020 chunk 111 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.128794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.097335 restraints weight = 22754.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.094460 restraints weight = 19632.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.095488 restraints weight = 20397.006| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.7047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10042 Z= 0.093 Angle : 0.563 7.987 13610 Z= 0.280 Chirality : 0.039 0.138 1574 Planarity : 0.004 0.064 1690 Dihedral : 4.537 47.786 1330 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.84 % Allowed : 20.56 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.24), residues: 1223 helix: -0.68 (0.20), residues: 699 sheet: 0.41 (0.57), residues: 79 loop : -1.33 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 64 HIS 0.003 0.001 HIS A 572 PHE 0.052 0.001 PHE A 369 TYR 0.027 0.001 TYR A 550 ARG 0.001 0.000 ARG A 706 Details of bonding type rmsd hydrogen bonds : bond 0.02938 ( 364) hydrogen bonds : angle 4.11337 ( 1053) covalent geometry : bond 0.00202 (10042) covalent geometry : angle 0.56339 (13610) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.7292 (ttp) cc_final: 0.7008 (ttp) REVERT: A 207 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7938 (mt0) REVERT: A 214 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.7953 (t80) REVERT: A 374 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8568 (tm-30) REVERT: A 409 MET cc_start: 0.7450 (pmm) cc_final: 0.5517 (mtp) REVERT: A 1166 MET cc_start: 0.4340 (pmm) cc_final: 0.2697 (mtm) REVERT: A 1259 TYR cc_start: 0.6325 (t80) cc_final: 0.6023 (t80) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.2226 time to fit residues: 21.7561 Evaluate side-chains 60 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 1028 GLN Chi-restraints excluded: chain A residue 1261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 101 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.125345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.093577 restraints weight = 23107.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.090608 restraints weight = 20676.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.091228 restraints weight = 23949.610| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.7404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10042 Z= 0.164 Angle : 0.635 8.251 13610 Z= 0.319 Chirality : 0.042 0.144 1574 Planarity : 0.004 0.059 1690 Dihedral : 4.835 44.025 1330 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.50 % Allowed : 20.09 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.24), residues: 1223 helix: -0.87 (0.20), residues: 715 sheet: 0.36 (0.57), residues: 79 loop : -1.40 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1147 HIS 0.006 0.001 HIS A 903 PHE 0.062 0.002 PHE A 369 TYR 0.014 0.001 TYR A 339 ARG 0.004 0.000 ARG A 824 Details of bonding type rmsd hydrogen bonds : bond 0.04709 ( 364) hydrogen bonds : angle 4.41257 ( 1053) covalent geometry : bond 0.00394 (10042) covalent geometry : angle 0.63461 (13610) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3195.64 seconds wall clock time: 57 minutes 14.88 seconds (3434.88 seconds total)