Starting phenix.real_space_refine on Sun Dec 29 05:57:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iz7_35834/12_2024/8iz7_35834_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iz7_35834/12_2024/8iz7_35834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iz7_35834/12_2024/8iz7_35834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iz7_35834/12_2024/8iz7_35834.map" model { file = "/net/cci-nas-00/data/ceres_data/8iz7_35834/12_2024/8iz7_35834_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iz7_35834/12_2024/8iz7_35834_trim.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.043 sd= 0.125 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 44 5.16 5 C 6385 2.51 5 N 1650 2.21 5 O 1750 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9830 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1229, 9805 Classifications: {'peptide': 1229} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 1190} Chain breaks: 2 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'SUZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.09, per 1000 atoms: 0.62 Number of scatterers: 9830 At special positions: 0 Unit cell: (76.54, 113.52, 161.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 F 1 9.00 O 1750 8.00 N 1650 7.00 C 6385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.2 seconds 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 4 sheets defined 60.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 17 through 23 Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 27 through 37 removed outlier: 3.686A pdb=" N LYS A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 44 removed outlier: 4.049A pdb=" N MET A 44 " --> pdb=" O GLU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 73 removed outlier: 4.177A pdb=" N GLU A 59 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 68 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG A 70 " --> pdb=" O LYS A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 removed outlier: 3.502A pdb=" N CYS A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 88 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 97 through 102 removed outlier: 3.767A pdb=" N ILE A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 102' Processing helix chain 'A' and resid 107 through 118 removed outlier: 3.989A pdb=" N ILE A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.611A pdb=" N ASN A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR A 123 " --> pdb=" O PHE A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 119 through 123' Processing helix chain 'A' and resid 127 through 145 removed outlier: 4.330A pdb=" N ALA A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR A 137 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'A' and resid 152 through 177 removed outlier: 3.829A pdb=" N ALA A 162 " --> pdb=" O HIS A 158 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET A 164 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR A 175 " --> pdb=" O CYS A 171 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 176 " --> pdb=" O HIS A 172 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS A 177 " --> pdb=" O MET A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 Processing helix chain 'A' and resid 190 through 195 removed outlier: 4.407A pdb=" N ILE A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 190 through 195' Processing helix chain 'A' and resid 204 through 212 removed outlier: 4.119A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 217 through 231 removed outlier: 3.861A pdb=" N GLN A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 237 through 261 removed outlier: 3.733A pdb=" N MET A 241 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 4.021A pdb=" N SER A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 255 " --> pdb=" O GLN A 251 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 257 " --> pdb=" O CYS A 253 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.882A pdb=" N THR A 267 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 removed outlier: 3.804A pdb=" N THR A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 291 through 303 removed outlier: 3.928A pdb=" N ASN A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 299 " --> pdb=" O PHE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 322 through 327 removed outlier: 3.674A pdb=" N SER A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.795A pdb=" N THR A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.938A pdb=" N ALA A 360 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 356 through 361' Processing helix chain 'A' and resid 370 through 375 Processing helix chain 'A' and resid 382 through 391 removed outlier: 4.552A pdb=" N THR A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 460 Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 500 through 512 Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 522 through 526 removed outlier: 3.589A pdb=" N LEU A 525 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR A 526 " --> pdb=" O GLY A 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 522 through 526' Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.527A pdb=" N GLY A 532 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR A 533 " --> pdb=" O ASP A 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 529 through 533' Processing helix chain 'A' and resid 536 through 551 Processing helix chain 'A' and resid 566 through 578 Processing helix chain 'A' and resid 580 through 584 removed outlier: 3.753A pdb=" N HIS A 583 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU A 584 " --> pdb=" O ILE A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 584' Processing helix chain 'A' and resid 593 through 597 removed outlier: 3.881A pdb=" N TYR A 596 " --> pdb=" O GLN A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 623 Processing helix chain 'A' and resid 626 through 632 removed outlier: 3.676A pdb=" N LEU A 630 " --> pdb=" O ASP A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 707 removed outlier: 3.944A pdb=" N TYR A 701 " --> pdb=" O GLY A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 730 removed outlier: 4.047A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ALA A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 730 " --> pdb=" O VAL A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 743 removed outlier: 3.771A pdb=" N LYS A 741 " --> pdb=" O TYR A 737 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 773 removed outlier: 3.533A pdb=" N TYR A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLY A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 removed outlier: 3.504A pdb=" N ILE A 780 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 776 through 781' Processing helix chain 'A' and resid 785 through 798 removed outlier: 3.628A pdb=" N SER A 794 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS A 798 " --> pdb=" O SER A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 803 removed outlier: 3.623A pdb=" N GLU A 803 " --> pdb=" O ASN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 removed outlier: 3.780A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 815 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 816 " --> pdb=" O PHE A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 856 removed outlier: 3.892A pdb=" N ASP A 842 " --> pdb=" O LEU A 838 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 843 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR A 846 " --> pdb=" O ASP A 842 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 848 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN A 849 " --> pdb=" O GLN A 845 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL A 853 " --> pdb=" O GLN A 849 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 854 " --> pdb=" O VAL A 850 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 855 " --> pdb=" O VAL A 851 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 867 No H-bonds generated for 'chain 'A' and resid 865 through 867' Processing helix chain 'A' and resid 868 through 883 removed outlier: 3.513A pdb=" N ARG A 880 " --> pdb=" O ILE A 876 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 896 removed outlier: 3.615A pdb=" N VAL A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 905 Processing helix chain 'A' and resid 924 through 936 removed outlier: 3.677A pdb=" N HIS A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 943 removed outlier: 3.868A pdb=" N PHE A 941 " --> pdb=" O ALA A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 949 removed outlier: 3.809A pdb=" N PHE A 948 " --> pdb=" O THR A 944 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 949 " --> pdb=" O SER A 945 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 944 through 949' Processing helix chain 'A' and resid 960 through 969 removed outlier: 3.547A pdb=" N ALA A 964 " --> pdb=" O VAL A 960 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY A 966 " --> pdb=" O ILE A 962 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 969 " --> pdb=" O PHE A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 974 removed outlier: 3.638A pdb=" N LEU A 974 " --> pdb=" O ALA A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 986 removed outlier: 3.537A pdb=" N LEU A 983 " --> pdb=" O VAL A 979 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 986 " --> pdb=" O ALA A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1006 removed outlier: 3.610A pdb=" N ARG A 998 " --> pdb=" O GLN A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1016 Processing helix chain 'A' and resid 1080 through 1089 removed outlier: 3.608A pdb=" N LEU A1084 " --> pdb=" O GLY A1080 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1115 Processing helix chain 'A' and resid 1130 through 1136 Processing helix chain 'A' and resid 1142 through 1153 Processing helix chain 'A' and resid 1156 through 1161 removed outlier: 3.978A pdb=" N ASP A1161 " --> pdb=" O GLU A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1175 removed outlier: 3.618A pdb=" N GLY A1174 " --> pdb=" O ALA A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1194 removed outlier: 3.507A pdb=" N LYS A1194 " --> pdb=" O ALA A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1222 Processing helix chain 'A' and resid 1257 through 1263 removed outlier: 3.587A pdb=" N GLN A1263 " --> pdb=" O TYR A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1275 removed outlier: 3.867A pdb=" N LYS A1271 " --> pdb=" O SER A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1297 Processing sheet with id=AA1, first strand: chain 'A' and resid 431 through 435 removed outlier: 7.265A pdb=" N PHE A 433 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLN A 413 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL A 435 " --> pdb=" O HIS A 411 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N HIS A 411 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL A 412 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N SER A 470 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ASP A 414 " --> pdb=" O LEU A 468 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU A 468 " --> pdb=" O ASP A 414 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.548A pdb=" N TYR A 556 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL A 590 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A 558 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN A 613 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS A 607 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N MET A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1061 through 1065 removed outlier: 5.872A pdb=" N LEU A1061 " --> pdb=" O ASN A1045 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A1045 " --> pdb=" O LEU A1061 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE A1043 " --> pdb=" O TRP A1099 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N TRP A1099 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN A1045 " --> pdb=" O LYS A1097 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A1097 " --> pdb=" O ASN A1045 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1118 through 1120 removed outlier: 3.578A pdb=" N VAL A1071 " --> pdb=" O VAL A1228 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A1230 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) 364 hydrogen bonds defined for protein. 1053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.37 Time building geometry restraints manager: 3.03 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.250 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.300 ------------------------------------------------------------------------------- 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= 0.279 Angle : 0.767 14.106 13610 Z= 0.508 Chirality : 0.038 0.123 1574 Planarity : 0.003 0.041 1690 Dihedral : 13.687 77.350 3662 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.19), residues: 1223 helix: -2.97 (0.15), residues: 697 sheet: -0.99 (0.50), residues: 80 loop : -2.70 (0.24), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 711 HIS 0.003 0.001 HIS A1111 PHE 0.003 0.000 PHE A 418 TYR 0.003 0.000 TYR A1259 ARG 0.001 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.6695 (mtm) cc_final: 0.5593 (mtp) REVERT: A 89 TRP cc_start: 0.6655 (p-90) cc_final: 0.5941 (t60) REVERT: A 98 PHE cc_start: 0.7342 (t80) cc_final: 0.6458 (m-10) REVERT: A 562 LEU cc_start: 0.7593 (mm) cc_final: 0.7227 (tt) REVERT: A 744 MET cc_start: 0.8166 (tmm) cc_final: 0.7897 (tpp) REVERT: A 763 TRP cc_start: 0.7548 (t-100) cc_final: 0.6872 (t60) REVERT: A 828 ASP cc_start: 0.7947 (p0) cc_final: 0.7717 (t70) REVERT: A 923 CYS cc_start: 0.7428 (m) cc_final: 0.6746 (m) REVERT: A 975 ASP cc_start: 0.6140 (p0) cc_final: 0.5691 (t0) REVERT: A 1026 GLU cc_start: 0.7713 (pm20) cc_final: 0.7463 (pp20) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2600 time to fit residues: 66.3419 Evaluate side-chains 87 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 0.0030 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 0.3980 chunk 110 optimal weight: 8.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 934 HIS A1141 HIS A1183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10042 Z= 0.184 Angle : 0.637 10.827 13610 Z= 0.313 Chirality : 0.041 0.238 1574 Planarity : 0.005 0.070 1690 Dihedral : 5.058 87.156 1330 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.78 % Allowed : 11.68 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.21), residues: 1223 helix: -1.91 (0.18), residues: 675 sheet: -0.08 (0.56), residues: 80 loop : -2.08 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 912 HIS 0.006 0.001 HIS A 172 PHE 0.046 0.001 PHE A 369 TYR 0.019 0.002 TYR A 768 ARG 0.004 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.5920 (tp) cc_final: 0.5666 (tp) REVERT: A 214 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7504 (t80) REVERT: A 288 MET cc_start: 0.7526 (ptt) cc_final: 0.7062 (ptm) REVERT: A 744 MET cc_start: 0.8166 (tmm) cc_final: 0.7918 (tpp) REVERT: A 820 ARG cc_start: 0.6491 (tpt170) cc_final: 0.6136 (tpm170) REVERT: A 975 ASP cc_start: 0.6537 (p0) cc_final: 0.6128 (t0) REVERT: A 1026 GLU cc_start: 0.7906 (pm20) cc_final: 0.7323 (pp20) REVERT: A 1195 ASN cc_start: 0.4221 (m-40) cc_final: 0.3614 (m-40) outliers start: 19 outliers final: 11 residues processed: 119 average time/residue: 0.2320 time to fit residues: 39.4548 Evaluate side-chains 92 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1261 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 0.0060 chunk 110 optimal weight: 8.9990 chunk 119 optimal weight: 20.0000 chunk 98 optimal weight: 0.0070 chunk 37 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 0.0370 overall best weight: 1.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS A1141 HIS A1181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10042 Z= 0.200 Angle : 0.619 10.848 13610 Z= 0.313 Chirality : 0.041 0.189 1574 Planarity : 0.004 0.055 1690 Dihedral : 5.281 88.632 1330 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.90 % Allowed : 13.36 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.23), residues: 1223 helix: -1.48 (0.19), residues: 697 sheet: 0.08 (0.56), residues: 80 loop : -1.78 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 230 HIS 0.005 0.001 HIS A 903 PHE 0.034 0.002 PHE A 369 TYR 0.016 0.002 TYR A 768 ARG 0.003 0.000 ARG A 165 *********************** 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 121 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.4860 (pmm) cc_final: 0.4182 (ptm) REVERT: A 207 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7437 (mt0) REVERT: A 214 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7650 (t80) REVERT: A 744 MET cc_start: 0.8082 (tmm) cc_final: 0.7836 (tpp) REVERT: A 820 ARG cc_start: 0.6998 (tpt170) cc_final: 0.6418 (tpm170) REVERT: A 1026 GLU cc_start: 0.8062 (pm20) cc_final: 0.7424 (pp20) REVERT: A 1166 MET cc_start: 0.0268 (pmm) cc_final: -0.0944 (mtm) outliers start: 31 outliers final: 19 residues processed: 112 average time/residue: 0.2077 time to fit residues: 34.1970 Evaluate side-chains 92 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1200 ILE Chi-restraints excluded: chain A residue 1237 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 74 optimal weight: 0.0370 chunk 111 optimal weight: 4.9990 chunk 117 optimal weight: 0.4980 chunk 58 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1141 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10042 Z= 0.162 Angle : 0.568 8.668 13610 Z= 0.284 Chirality : 0.040 0.172 1574 Planarity : 0.004 0.059 1690 Dihedral : 5.035 80.152 1330 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.06 % Allowed : 15.61 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.23), residues: 1223 helix: -1.26 (0.19), residues: 701 sheet: 0.24 (0.56), residues: 80 loop : -1.65 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 711 HIS 0.003 0.001 HIS A 903 PHE 0.024 0.001 PHE A 369 TYR 0.025 0.001 TYR A1259 ARG 0.002 0.000 ARG A 706 *********************** 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 91 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLN cc_start: 0.7727 (mm-40) cc_final: 0.7384 (mt0) REVERT: A 214 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.7696 (t80) REVERT: A 744 MET cc_start: 0.8062 (tmm) cc_final: 0.7812 (tpp) REVERT: A 820 ARG cc_start: 0.6939 (tpt170) cc_final: 0.6224 (tpm170) REVERT: A 1026 GLU cc_start: 0.7980 (pm20) cc_final: 0.7339 (pp20) REVERT: A 1166 MET cc_start: 0.0979 (pmm) cc_final: -0.0677 (mtm) outliers start: 22 outliers final: 15 residues processed: 85 average time/residue: 0.1827 time to fit residues: 24.3323 Evaluate side-chains 81 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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 89 TRP 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 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 985 TYR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1261 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 0.0030 chunk 100 optimal weight: 30.0000 chunk 81 optimal weight: 0.0770 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 overall best weight: 0.8154 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.5385 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= 0.128 Angle : 0.548 8.891 13610 Z= 0.270 Chirality : 0.039 0.159 1574 Planarity : 0.004 0.052 1690 Dihedral : 4.893 80.676 1330 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.68 % Allowed : 17.10 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.24), residues: 1223 helix: -1.06 (0.20), residues: 702 sheet: 0.32 (0.56), residues: 80 loop : -1.52 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 711 HIS 0.003 0.001 HIS A 572 PHE 0.022 0.001 PHE A 369 TYR 0.012 0.001 TYR A1255 ARG 0.002 0.000 ARG A 824 *********************** 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 87 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.6843 (ttp) cc_final: 0.6597 (ttp) REVERT: A 207 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7380 (mt0) REVERT: A 214 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.7685 (t80) REVERT: A 744 MET cc_start: 0.8055 (tmm) cc_final: 0.7799 (tpp) REVERT: A 820 ARG cc_start: 0.6939 (tpt170) cc_final: 0.6216 (tpm170) REVERT: A 1026 GLU cc_start: 0.7956 (pm20) cc_final: 0.7281 (pp20) REVERT: A 1166 MET cc_start: 0.1103 (pmm) cc_final: -0.0653 (mtm) outliers start: 18 outliers final: 12 residues processed: 81 average time/residue: 0.1856 time to fit residues: 23.4824 Evaluate side-chains 76 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 89 TRP Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 245 ILE 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 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 106 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 0.0570 chunk 118 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 overall best weight: 2.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1037 HIS A1141 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.6434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10042 Z= 0.243 Angle : 0.647 8.956 13610 Z= 0.326 Chirality : 0.043 0.177 1574 Planarity : 0.004 0.059 1690 Dihedral : 5.248 72.696 1330 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.15 % Allowed : 17.66 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.24), residues: 1223 helix: -1.15 (0.19), residues: 713 sheet: 0.29 (0.55), residues: 80 loop : -1.64 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 711 HIS 0.005 0.001 HIS A 903 PHE 0.019 0.002 PHE A 369 TYR 0.019 0.002 TYR A 556 ARG 0.004 0.000 ARG A 547 *********************** 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 92 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7551 (mtt90) cc_final: 0.7187 (mtp85) REVERT: A 207 GLN cc_start: 0.8367 (mm-40) cc_final: 0.7729 (mt0) REVERT: A 214 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.7699 (t80) REVERT: A 744 MET cc_start: 0.8028 (tmm) cc_final: 0.7685 (tpp) REVERT: A 1026 GLU cc_start: 0.7990 (pm20) cc_final: 0.7533 (mp0) REVERT: A 1166 MET cc_start: 0.2232 (pmm) cc_final: 0.0814 (mtm) REVERT: A 1259 TYR cc_start: 0.5669 (t80) cc_final: 0.5408 (t80) outliers start: 23 outliers final: 13 residues processed: 87 average time/residue: 0.1928 time to fit residues: 25.8911 Evaluate side-chains 74 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 1040 VAL 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 13 optimal weight: 0.9980 chunk 67 optimal weight: 0.0470 chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 0.0870 chunk 99 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1233 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.6435 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= 0.124 Angle : 0.549 8.820 13610 Z= 0.272 Chirality : 0.039 0.153 1574 Planarity : 0.004 0.056 1690 Dihedral : 4.755 68.805 1330 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.21 % Allowed : 19.07 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.24), residues: 1223 helix: -0.87 (0.20), residues: 708 sheet: 0.33 (0.55), residues: 80 loop : -1.36 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 64 HIS 0.010 0.001 HIS A1233 PHE 0.015 0.001 PHE A 369 TYR 0.011 0.001 TYR A1255 ARG 0.002 0.000 ARG A 824 *********************** 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 82 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.6836 (ttp) cc_final: 0.6599 (ttp) REVERT: A 207 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7737 (mt0) REVERT: A 214 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7675 (t80) REVERT: A 744 MET cc_start: 0.8016 (tmm) cc_final: 0.7716 (tpp) REVERT: A 820 ARG cc_start: 0.6948 (tpt170) cc_final: 0.6352 (tpm170) REVERT: A 1026 GLU cc_start: 0.7992 (pm20) cc_final: 0.7604 (mp0) REVERT: A 1166 MET cc_start: 0.2426 (pmm) cc_final: 0.0951 (mtm) REVERT: A 1259 TYR cc_start: 0.5582 (t80) cc_final: 0.5342 (t80) outliers start: 13 outliers final: 10 residues processed: 78 average time/residue: 0.1925 time to fit residues: 23.2632 Evaluate side-chains 74 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 245 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1261 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 3.9990 chunk 70 optimal weight: 0.0000 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 0.0470 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10042 Z= 0.132 Angle : 0.549 8.071 13610 Z= 0.270 Chirality : 0.039 0.141 1574 Planarity : 0.003 0.055 1690 Dihedral : 4.554 65.034 1330 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.50 % Allowed : 19.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.24), residues: 1223 helix: -0.80 (0.20), residues: 715 sheet: 0.36 (0.56), residues: 80 loop : -1.31 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.003 0.001 HIS A 572 PHE 0.016 0.001 PHE A 369 TYR 0.025 0.001 TYR A 550 ARG 0.002 0.000 ARG A 824 *********************** 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 78 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 THR cc_start: 0.7906 (t) cc_final: 0.7591 (m) REVERT: A 207 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7713 (mt0) REVERT: A 214 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7691 (t80) REVERT: A 744 MET cc_start: 0.8024 (tmm) cc_final: 0.7723 (tpp) REVERT: A 1026 GLU cc_start: 0.7951 (pm20) cc_final: 0.7631 (mp0) REVERT: A 1049 MET cc_start: 0.7703 (mpp) cc_final: 0.7448 (mpp) REVERT: A 1166 MET cc_start: 0.2543 (pmm) cc_final: 0.1133 (mtm) REVERT: A 1259 TYR cc_start: 0.5666 (t80) cc_final: 0.5421 (t80) outliers start: 16 outliers final: 12 residues processed: 73 average time/residue: 0.1913 time to fit residues: 21.6509 Evaluate side-chains 73 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 89 TRP Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 1028 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1181 GLN 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 112 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 109 optimal weight: 0.0270 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 115 optimal weight: 0.0870 overall best weight: 1.1618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.6656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10042 Z= 0.147 Angle : 0.551 7.675 13610 Z= 0.273 Chirality : 0.039 0.134 1574 Planarity : 0.004 0.057 1690 Dihedral : 4.537 61.042 1330 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.40 % Allowed : 19.63 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.24), residues: 1223 helix: -0.73 (0.20), residues: 715 sheet: 0.43 (0.57), residues: 80 loop : -1.28 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 711 HIS 0.003 0.001 HIS A 572 PHE 0.015 0.001 PHE A 369 TYR 0.009 0.001 TYR A1255 ARG 0.002 0.000 ARG A1182 *********************** 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 77 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 THR cc_start: 0.7949 (t) cc_final: 0.7657 (m) REVERT: A 207 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7739 (mt0) REVERT: A 214 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7687 (t80) REVERT: A 744 MET cc_start: 0.8004 (tmm) cc_final: 0.7683 (tpp) REVERT: A 820 ARG cc_start: 0.6887 (tpt170) cc_final: 0.6417 (tpt170) REVERT: A 1026 GLU cc_start: 0.7954 (pm20) cc_final: 0.7645 (mp0) REVERT: A 1049 MET cc_start: 0.7750 (mpp) cc_final: 0.7545 (mpp) REVERT: A 1166 MET cc_start: 0.2582 (pmm) cc_final: 0.1273 (mtm) REVERT: A 1259 TYR cc_start: 0.5683 (t80) cc_final: 0.5417 (t80) outliers start: 15 outliers final: 13 residues processed: 74 average time/residue: 0.1937 time to fit residues: 22.4939 Evaluate side-chains 75 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 89 TRP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 1028 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1181 GLN Chi-restraints excluded: chain A residue 1261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.4980 chunk 54 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 121 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 76 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.6744 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= 0.136 Angle : 0.552 8.224 13610 Z= 0.271 Chirality : 0.039 0.131 1574 Planarity : 0.003 0.056 1690 Dihedral : 4.428 56.659 1330 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.12 % Allowed : 19.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.25), residues: 1223 helix: -0.68 (0.20), residues: 715 sheet: 0.49 (0.59), residues: 80 loop : -1.22 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 711 HIS 0.003 0.001 HIS A 572 PHE 0.015 0.001 PHE A 369 TYR 0.027 0.001 TYR A 550 ARG 0.003 0.000 ARG A1182 ********************** 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 75 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 THR cc_start: 0.7955 (t) cc_final: 0.7675 (m) REVERT: A 207 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7713 (mt0) REVERT: A 214 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7751 (t80) REVERT: A 374 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8699 (tm-30) REVERT: A 744 MET cc_start: 0.7986 (tmm) cc_final: 0.7665 (tpp) REVERT: A 820 ARG cc_start: 0.6865 (tpt170) cc_final: 0.6429 (tpt170) REVERT: A 1026 GLU cc_start: 0.7939 (pm20) cc_final: 0.7662 (mp0) REVERT: A 1049 MET cc_start: 0.7759 (mpp) cc_final: 0.7556 (mpp) REVERT: A 1166 MET cc_start: 0.2667 (pmm) cc_final: 0.1455 (mtm) REVERT: A 1259 TYR cc_start: 0.5726 (t80) cc_final: 0.5475 (t80) outliers start: 12 outliers final: 10 residues processed: 72 average time/residue: 0.1860 time to fit residues: 21.1137 Evaluate side-chains 72 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 89 TRP Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 544 ASN A1181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.130366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.098753 restraints weight = 22906.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.095591 restraints weight = 19922.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.096717 restraints weight = 21105.828| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.6866 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= 0.138 Angle : 0.554 8.421 13610 Z= 0.274 Chirality : 0.039 0.134 1574 Planarity : 0.003 0.057 1690 Dihedral : 4.326 48.517 1330 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.87 % Allowed : 19.44 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.25), residues: 1223 helix: -0.58 (0.21), residues: 715 sheet: 0.54 (0.59), residues: 80 loop : -1.18 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.003 0.001 HIS A 572 PHE 0.041 0.001 PHE A 369 TYR 0.009 0.001 TYR A1255 ARG 0.001 0.000 ARG A 824 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1867.71 seconds wall clock time: 35 minutes 1.76 seconds (2101.76 seconds total)