Starting phenix.real_space_refine on Fri Oct 10 23:47:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iz7_35834/10_2025/8iz7_35834_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iz7_35834/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8iz7_35834/10_2025/8iz7_35834_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iz7_35834/10_2025/8iz7_35834_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iz7_35834/10_2025/8iz7_35834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iz7_35834/10_2025/8iz7_35834.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 2.45, per 1000 atoms: 0.25 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: 0.96 Conformation dependent library (CDL) restraints added in 391.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.49 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: 1.64 Time building geometry restraints manager: 1.24 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: 1.990 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.010 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.660 ------------------------------------------------------------------------------- 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 : 6.38 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG A 375 TYR 0.003 0.000 TYR A1259 PHE 0.003 0.000 PHE A 418 TRP 0.004 0.000 TRP A 711 HIS 0.003 0.001 HIS A1111 Details of bonding type rmsd covalent geometry : bond 0.00445 (10042) covalent geometry : angle 0.76743 (13610) hydrogen bonds : bond 0.23771 ( 364) hydrogen bonds : angle 6.98247 ( 1053) *********************** 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 : 0.428 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: 0.6457 (m-10) REVERT: A 562 LEU cc_start: 0.7593 (mm) cc_final: 0.7226 (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: 0.6871 (t60) REVERT: A 828 ASP cc_start: 0.7947 (p0) cc_final: 0.7718 (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) REVERT: A 1061 LEU cc_start: 0.6765 (tt) cc_final: 0.6521 (pp) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1236 time to fit residues: 31.3977 Evaluate side-chains 90 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 73 ASN A 122 ASN A 153 HIS A 710 HIS A1141 HIS A1183 GLN A1296 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.126720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.093440 restraints weight = 23121.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.091071 restraints weight = 18389.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.091752 restraints weight = 21162.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.092222 restraints weight = 15417.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.092495 restraints weight = 13831.195| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 10042 Z= 0.298 Angle : 0.850 11.025 13610 Z= 0.431 Chirality : 0.050 0.326 1574 Planarity : 0.006 0.078 1690 Dihedral : 5.921 82.418 1330 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.52 % Favored : 92.40 % Rotamer: Outliers : 2.99 % Allowed : 13.36 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.36 (0.21), residues: 1223 helix: -2.29 (0.17), residues: 706 sheet: -0.24 (0.55), residues: 80 loop : -2.21 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 165 TYR 0.031 0.003 TYR A 768 PHE 0.041 0.003 PHE A 369 TRP 0.019 0.002 TRP A 763 HIS 0.009 0.002 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00713 (10042) covalent geometry : angle 0.85037 (13610) hydrogen bonds : bond 0.07394 ( 364) hydrogen bonds : angle 5.12617 ( 1053) *********************** 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 130 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.5251 (pmm) cc_final: 0.4607 (ptm) REVERT: A 214 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7931 (t80) REVERT: A 475 ILE cc_start: 0.8858 (mt) cc_final: 0.8609 (mm) REVERT: A 542 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.7615 (ptm160) REVERT: A 556 TYR cc_start: 0.6592 (m-80) cc_final: 0.6307 (m-80) REVERT: A 1026 GLU cc_start: 0.7920 (pm20) cc_final: 0.7581 (pp20) REVERT: A 1061 LEU cc_start: 0.7483 (tt) cc_final: 0.7116 (pp) REVERT: A 1065 ILE cc_start: 0.7445 (mm) cc_final: 0.7224 (mm) REVERT: A 1068 GLN cc_start: 0.6919 (mt0) cc_final: 0.6709 (pp30) outliers start: 32 outliers final: 18 residues processed: 125 average time/residue: 0.0912 time to fit residues: 16.6623 Evaluate side-chains 85 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 845 GLN Chi-restraints excluded: chain A residue 985 TYR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1125 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 7 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 60 optimal weight: 30.0000 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 100 optimal weight: 0.6980 chunk 56 optimal weight: 0.0270 overall best weight: 0.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1151 GLN A1181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.132167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.099283 restraints weight = 22577.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.096565 restraints weight = 18423.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.097416 restraints weight = 20317.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.097954 restraints weight = 14115.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.098165 restraints weight = 12961.122| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.5039 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= 0.100 Angle : 0.585 9.076 13610 Z= 0.294 Chirality : 0.039 0.149 1574 Planarity : 0.004 0.063 1690 Dihedral : 5.239 80.989 1330 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.68 % Allowed : 16.64 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.56 (0.23), residues: 1223 helix: -1.64 (0.19), residues: 698 sheet: 0.15 (0.57), residues: 80 loop : -1.92 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 284 TYR 0.018 0.001 TYR A1255 PHE 0.040 0.001 PHE A 369 TRP 0.013 0.001 TRP A 89 HIS 0.004 0.001 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00209 (10042) covalent geometry : angle 0.58518 (13610) hydrogen bonds : bond 0.03498 ( 364) hydrogen bonds : angle 4.34779 ( 1053) *********************** 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 93 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.7856 (t80) REVERT: A 409 MET cc_start: 0.7167 (pmm) cc_final: 0.5297 (mtp) REVERT: A 556 TYR cc_start: 0.6665 (m-80) cc_final: 0.6340 (m-80) REVERT: A 1007 MET cc_start: 0.8690 (tpt) cc_final: 0.8486 (tpp) REVERT: A 1026 GLU cc_start: 0.7747 (pm20) cc_final: 0.7364 (pp20) REVERT: A 1061 LEU cc_start: 0.7498 (tt) cc_final: 0.7153 (pp) REVERT: A 1068 GLN cc_start: 0.6846 (mt0) cc_final: 0.6624 (pp30) REVERT: A 1245 MET cc_start: 0.4602 (mtt) cc_final: 0.4220 (mtt) outliers start: 18 outliers final: 10 residues processed: 89 average time/residue: 0.0840 time to fit residues: 11.4667 Evaluate side-chains 77 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 233 ILE 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 710 HIS Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 1040 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 31 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 60 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 518 GLN A1037 HIS A1141 HIS A1181 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.125181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.091930 restraints weight = 22676.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.089838 restraints weight = 18893.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.090564 restraints weight = 19439.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.091079 restraints weight = 14538.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.091392 restraints weight = 13183.152| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10042 Z= 0.152 Angle : 0.627 9.236 13610 Z= 0.315 Chirality : 0.042 0.218 1574 Planarity : 0.004 0.061 1690 Dihedral : 5.221 74.450 1330 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.80 % Allowed : 18.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.23), residues: 1223 helix: -1.40 (0.19), residues: 709 sheet: 0.29 (0.57), residues: 80 loop : -1.91 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1132 TYR 0.016 0.002 TYR A 768 PHE 0.030 0.002 PHE A 369 TRP 0.012 0.001 TRP A 711 HIS 0.004 0.001 HIS A 903 Details of bonding type rmsd covalent geometry : bond 0.00358 (10042) covalent geometry : angle 0.62747 (13610) hydrogen bonds : bond 0.04789 ( 364) hydrogen bonds : angle 4.43526 ( 1053) *********************** 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 96 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7706 (mtt90) cc_final: 0.7450 (mtp85) REVERT: A 214 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.7894 (t80) REVERT: A 475 ILE cc_start: 0.8975 (mt) cc_final: 0.8723 (mm) REVERT: A 556 TYR cc_start: 0.6845 (m-80) cc_final: 0.6436 (m-80) REVERT: A 1061 LEU cc_start: 0.7829 (tt) cc_final: 0.7446 (pp) REVERT: A 1065 ILE cc_start: 0.7490 (mm) cc_final: 0.7266 (mm) REVERT: A 1166 MET cc_start: 0.3110 (pmm) cc_final: 0.1200 (mtm) REVERT: A 1259 TYR cc_start: 0.6799 (t80) cc_final: 0.6534 (t80) outliers start: 30 outliers final: 13 residues processed: 91 average time/residue: 0.0907 time to fit residues: 12.3986 Evaluate side-chains 72 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL 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 254 PHE Chi-restraints excluded: chain A residue 279 VAL 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 985 TYR Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 1040 VAL 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 101 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 40.0000 chunk 42 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.127731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.094913 restraints weight = 23110.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.092606 restraints weight = 19151.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.093315 restraints weight = 21278.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.093771 restraints weight = 14696.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.094081 restraints weight = 13461.462| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.6230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10042 Z= 0.115 Angle : 0.573 9.040 13610 Z= 0.286 Chirality : 0.040 0.191 1574 Planarity : 0.004 0.060 1690 Dihedral : 4.982 70.240 1330 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.68 % Allowed : 19.25 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.24), residues: 1223 helix: -1.31 (0.19), residues: 715 sheet: 0.27 (0.56), residues: 80 loop : -1.71 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 824 TYR 0.013 0.001 TYR A1255 PHE 0.023 0.001 PHE A 369 TRP 0.011 0.001 TRP A 711 HIS 0.003 0.001 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00263 (10042) covalent geometry : angle 0.57302 (13610) hydrogen bonds : bond 0.03788 ( 364) hydrogen bonds : angle 4.36449 ( 1053) *********************** 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 82 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.7183 (ttp) cc_final: 0.6921 (ttp) REVERT: A 214 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.7933 (t80) REVERT: A 475 ILE cc_start: 0.8984 (mt) cc_final: 0.8733 (mm) REVERT: A 556 TYR cc_start: 0.6938 (m-80) cc_final: 0.6533 (m-80) REVERT: A 1061 LEU cc_start: 0.7766 (tt) cc_final: 0.7285 (pp) REVERT: A 1065 ILE cc_start: 0.7568 (mm) cc_final: 0.7323 (mm) REVERT: A 1166 MET cc_start: 0.3501 (pmm) cc_final: 0.1565 (mtm) REVERT: A 1259 TYR cc_start: 0.6619 (t80) cc_final: 0.6344 (t80) outliers start: 18 outliers final: 12 residues processed: 77 average time/residue: 0.0798 time to fit residues: 9.7077 Evaluate side-chains 71 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 388 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 710 HIS 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 1261 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 95 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 60 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 924 GLN A1183 GLN A1233 HIS A1296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.123636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.092114 restraints weight = 23312.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.088940 restraints weight = 21682.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.089841 restraints weight = 26460.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.090432 restraints weight = 17136.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.090838 restraints weight = 15149.239| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.7141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10042 Z= 0.212 Angle : 0.699 8.338 13610 Z= 0.354 Chirality : 0.045 0.225 1574 Planarity : 0.005 0.064 1690 Dihedral : 5.499 61.630 1330 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.43 % Allowed : 19.44 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.23), residues: 1223 helix: -1.39 (0.19), residues: 702 sheet: 0.28 (0.57), residues: 80 loop : -1.93 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1132 TYR 0.016 0.002 TYR A 339 PHE 0.020 0.002 PHE A 369 TRP 0.016 0.002 TRP A 711 HIS 0.008 0.001 HIS A1233 Details of bonding type rmsd covalent geometry : bond 0.00510 (10042) covalent geometry : angle 0.69915 (13610) hydrogen bonds : bond 0.05849 ( 364) hydrogen bonds : angle 4.80034 ( 1053) *********************** 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 82 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7668 (mtt90) cc_final: 0.7398 (mtp85) REVERT: A 214 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.7893 (t80) REVERT: A 475 ILE cc_start: 0.9047 (mt) cc_final: 0.8843 (mm) REVERT: A 556 TYR cc_start: 0.7016 (m-80) cc_final: 0.6566 (m-80) REVERT: A 1065 ILE cc_start: 0.7443 (mm) cc_final: 0.7177 (mm) REVERT: A 1166 MET cc_start: 0.4145 (pmm) cc_final: 0.2794 (mtm) REVERT: A 1259 TYR cc_start: 0.6720 (t80) cc_final: 0.6387 (t80) outliers start: 26 outliers final: 14 residues processed: 78 average time/residue: 0.0884 time to fit residues: 10.5778 Evaluate side-chains 66 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL 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 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 773 VAL Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1237 THR 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 51 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 102 optimal weight: 0.1980 chunk 39 optimal weight: 9.9990 chunk 61 optimal weight: 40.0000 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.126544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.094842 restraints weight = 23042.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.092665 restraints weight = 22012.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.093174 restraints weight = 25813.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.093836 restraints weight = 16284.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.094361 restraints weight = 14243.239| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.7154 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 : 0.589 7.909 13610 Z= 0.293 Chirality : 0.041 0.181 1574 Planarity : 0.004 0.063 1690 Dihedral : 4.977 54.136 1330 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.78 % Allowed : 20.56 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.24), residues: 1223 helix: -1.17 (0.20), residues: 708 sheet: 0.27 (0.56), residues: 80 loop : -1.71 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1132 TYR 0.012 0.001 TYR A1255 PHE 0.020 0.001 PHE A 369 TRP 0.013 0.001 TRP A 711 HIS 0.003 0.001 HIS A1037 Details of bonding type rmsd covalent geometry : bond 0.00255 (10042) covalent geometry : angle 0.58861 (13610) hydrogen bonds : bond 0.03845 ( 364) hydrogen bonds : angle 4.39114 ( 1053) *********************** 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 74 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7660 (mtt90) cc_final: 0.7438 (mtp85) REVERT: A 164 MET cc_start: 0.7355 (ttp) cc_final: 0.7086 (ttp) REVERT: A 214 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.7932 (t80) REVERT: A 374 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8561 (tm-30) REVERT: A 820 ARG cc_start: 0.7499 (tpt170) cc_final: 0.7293 (tpt170) REVERT: A 1166 MET cc_start: 0.4125 (pmm) cc_final: 0.2663 (mtm) REVERT: A 1259 TYR cc_start: 0.6671 (t80) cc_final: 0.6349 (t80) outliers start: 19 outliers final: 14 residues processed: 72 average time/residue: 0.0876 time to fit residues: 9.7051 Evaluate side-chains 63 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 190 THR 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 710 HIS Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 985 TYR Chi-restraints excluded: chain A residue 1085 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 93 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.127629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.095964 restraints weight = 22951.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.093068 restraints weight = 20769.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.094101 restraints weight = 23498.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.094665 restraints weight = 15779.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.095083 restraints weight = 14196.648| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.7208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10042 Z= 0.100 Angle : 0.564 7.938 13610 Z= 0.279 Chirality : 0.040 0.242 1574 Planarity : 0.004 0.061 1690 Dihedral : 4.660 47.319 1330 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.96 % Allowed : 20.93 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.24), residues: 1223 helix: -1.04 (0.20), residues: 712 sheet: 0.24 (0.57), residues: 79 loop : -1.60 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 706 TYR 0.012 0.001 TYR A1255 PHE 0.018 0.001 PHE A 369 TRP 0.011 0.001 TRP A 64 HIS 0.004 0.001 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00223 (10042) covalent geometry : angle 0.56437 (13610) hydrogen bonds : bond 0.03307 ( 364) hydrogen bonds : angle 4.28720 ( 1053) *********************** 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 70 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7614 (mtt90) cc_final: 0.7400 (mtp85) REVERT: A 164 MET cc_start: 0.7270 (ttp) cc_final: 0.6998 (ttp) REVERT: A 214 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.7933 (t80) REVERT: A 374 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8585 (tm-30) REVERT: A 409 MET cc_start: 0.7380 (pmm) cc_final: 0.5419 (mtp) REVERT: A 1166 MET cc_start: 0.4242 (pmm) cc_final: 0.2848 (mtm) REVERT: A 1259 TYR cc_start: 0.6623 (t80) cc_final: 0.6328 (t80) outliers start: 21 outliers final: 13 residues processed: 67 average time/residue: 0.0916 time to fit residues: 9.4327 Evaluate side-chains 65 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 710 HIS Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 761 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 1085 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 44 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 115 optimal weight: 0.0670 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 91 optimal weight: 0.0370 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 849 GLN A 903 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.129020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.097146 restraints weight = 22842.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.094232 restraints weight = 19932.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.095177 restraints weight = 18803.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.095853 restraints weight = 14431.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.095967 restraints weight = 13555.228| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.7204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10042 Z= 0.089 Angle : 0.550 7.911 13610 Z= 0.272 Chirality : 0.039 0.258 1574 Planarity : 0.004 0.059 1690 Dihedral : 4.414 41.979 1330 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.40 % Allowed : 21.96 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.24), residues: 1223 helix: -0.83 (0.20), residues: 705 sheet: 0.08 (0.57), residues: 80 loop : -1.45 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 824 TYR 0.012 0.001 TYR A1255 PHE 0.017 0.001 PHE A 369 TRP 0.012 0.001 TRP A 64 HIS 0.004 0.001 HIS A 710 Details of bonding type rmsd covalent geometry : bond 0.00189 (10042) covalent geometry : angle 0.54975 (13610) hydrogen bonds : bond 0.02754 ( 364) hydrogen bonds : angle 4.14697 ( 1053) *********************** 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 66 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.7181 (ttp) cc_final: 0.6924 (ttp) REVERT: A 186 MET cc_start: 0.8276 (ttp) cc_final: 0.7814 (tpt) REVERT: A 214 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7897 (t80) REVERT: A 374 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8637 (tm-30) REVERT: A 409 MET cc_start: 0.7294 (pmm) cc_final: 0.5266 (mtp) REVERT: A 1166 MET cc_start: 0.4019 (pmm) cc_final: 0.2565 (mtm) REVERT: A 1259 TYR cc_start: 0.6515 (t80) cc_final: 0.6242 (t80) outliers start: 15 outliers final: 11 residues processed: 64 average time/residue: 0.0772 time to fit residues: 8.0140 Evaluate side-chains 61 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 68 VAL 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 710 HIS 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 1261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 3 optimal weight: 3.9990 chunk 115 optimal weight: 0.0980 chunk 121 optimal weight: 30.0000 chunk 47 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 90 optimal weight: 0.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.127938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.096114 restraints weight = 22709.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.092875 restraints weight = 18731.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.093782 restraints weight = 19571.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.094832 restraints weight = 14602.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.094854 restraints weight = 12653.563| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.7315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10042 Z= 0.101 Angle : 0.558 8.592 13610 Z= 0.276 Chirality : 0.040 0.229 1574 Planarity : 0.004 0.060 1690 Dihedral : 4.375 37.130 1330 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.40 % Allowed : 22.06 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.24), residues: 1223 helix: -0.74 (0.20), residues: 701 sheet: 0.17 (0.58), residues: 80 loop : -1.41 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 706 TYR 0.011 0.001 TYR A1255 PHE 0.017 0.001 PHE A 369 TRP 0.013 0.001 TRP A 711 HIS 0.004 0.001 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00229 (10042) covalent geometry : angle 0.55826 (13610) hydrogen bonds : bond 0.03310 ( 364) hydrogen bonds : angle 4.16781 ( 1053) ********************** 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 67 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.7336 (ttp) cc_final: 0.7052 (ttp) REVERT: A 186 MET cc_start: 0.8302 (ttp) cc_final: 0.7855 (tpt) REVERT: A 214 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.7898 (t80) REVERT: A 374 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8613 (tm-30) REVERT: A 556 TYR cc_start: 0.6805 (m-80) cc_final: 0.6229 (m-80) REVERT: A 1166 MET cc_start: 0.4251 (pmm) cc_final: 0.2926 (mtm) REVERT: A 1259 TYR cc_start: 0.6535 (t80) cc_final: 0.6247 (t80) outliers start: 15 outliers final: 12 residues processed: 65 average time/residue: 0.0737 time to fit residues: 7.9455 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 : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 68 VAL 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 710 HIS Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 851 VAL 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 1261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 70 optimal weight: 0.0070 chunk 44 optimal weight: 5.9990 chunk 46 optimal weight: 0.0980 chunk 41 optimal weight: 5.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.128870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.096916 restraints weight = 22900.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.094222 restraints weight = 19301.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.095212 restraints weight = 22769.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.095760 restraints weight = 15000.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.096269 restraints weight = 13426.179| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.7336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10042 Z= 0.090 Angle : 0.547 7.989 13610 Z= 0.270 Chirality : 0.039 0.229 1574 Planarity : 0.004 0.059 1690 Dihedral : 4.275 35.528 1330 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.50 % Allowed : 21.78 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.25), residues: 1223 helix: -0.67 (0.20), residues: 702 sheet: 0.18 (0.58), residues: 80 loop : -1.34 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 706 TYR 0.030 0.001 TYR A 550 PHE 0.017 0.001 PHE A 433 TRP 0.011 0.001 TRP A 711 HIS 0.004 0.001 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00196 (10042) covalent geometry : angle 0.54748 (13610) hydrogen bonds : bond 0.02902 ( 364) hydrogen bonds : angle 4.09255 ( 1053) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1567.74 seconds wall clock time: 27 minutes 51.48 seconds (1671.48 seconds total)