Starting phenix.real_space_refine on Sat Aug 23 02:25:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpx_60366/08_2025/8zpx_60366.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpx_60366/08_2025/8zpx_60366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zpx_60366/08_2025/8zpx_60366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpx_60366/08_2025/8zpx_60366.map" model { file = "/net/cci-nas-00/data/ceres_data/8zpx_60366/08_2025/8zpx_60366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpx_60366/08_2025/8zpx_60366.cif" } resolution = 3.5 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= 0.001 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 5798 2.51 5 N 1555 2.21 5 O 1669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9065 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 9065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1178, 9065 Classifications: {'peptide': 1178} Link IDs: {'PTRANS': 30, 'TRANS': 1147} Chain breaks: 1 Time building chain proxies: 1.77, per 1000 atoms: 0.20 Number of scatterers: 9065 At special positions: 0 Unit cell: (73.7, 106.7, 144.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1669 8.00 N 1555 7.00 C 5798 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: 0.67 Conformation dependent library (CDL) restraints added in 311.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 5 sheets defined 57.8% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 39 through 56 removed outlier: 3.862A pdb=" N GLY B 45 " --> pdb=" O TYR B 41 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B 48 " --> pdb=" O MET B 44 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 71 removed outlier: 3.666A pdb=" N ARG B 63 " --> pdb=" O PRO B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 91 Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 97 through 113 removed outlier: 3.622A pdb=" N TRP B 101 " --> pdb=" O GLY B 97 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 107 " --> pdb=" O SER B 103 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 108 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 109 " --> pdb=" O TRP B 105 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N CYS B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 129 removed outlier: 3.660A pdb=" N LYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 143 through 148 removed outlier: 3.727A pdb=" N VAL B 148 " --> pdb=" O THR B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 152 Processing helix chain 'B' and resid 153 through 163 removed outlier: 4.024A pdb=" N VAL B 158 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 185 removed outlier: 3.677A pdb=" N ILE B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 176 " --> pdb=" O TYR B 172 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 180 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 4.127A pdb=" N VAL B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 214 removed outlier: 4.019A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR B 209 " --> pdb=" O GLY B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 226 removed outlier: 3.904A pdb=" N SER B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N SER B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 236 removed outlier: 3.612A pdb=" N VAL B 234 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN B 236 " --> pdb=" O GLN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 removed outlier: 3.881A pdb=" N MET B 241 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA B 242 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.904A pdb=" N SER B 255 " --> pdb=" O GLN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 263 removed outlier: 3.654A pdb=" N LEU B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 278 through 299 removed outlier: 3.852A pdb=" N CYS B 284 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU B 288 " --> pdb=" O CYS B 284 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 289 " --> pdb=" O CYS B 285 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TRP B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 298 " --> pdb=" O GLY B 294 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS B 299 " --> pdb=" O TYR B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.664A pdb=" N ALA B 307 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 308 " --> pdb=" O GLY B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 308' Processing helix chain 'B' and resid 311 through 316 Processing helix chain 'B' and resid 321 through 324 Processing helix chain 'B' and resid 325 through 334 removed outlier: 3.701A pdb=" N ALA B 330 " --> pdb=" O PRO B 326 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE B 331 " --> pdb=" O SER B 327 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B 332 " --> pdb=" O MET B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 removed outlier: 3.512A pdb=" N PHE B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 417 removed outlier: 4.230A pdb=" N GLU B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.513A pdb=" N ILE B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 468 Processing helix chain 'B' and resid 472 through 481 removed outlier: 3.518A pdb=" N GLU B 477 " --> pdb=" O GLN B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 490 removed outlier: 3.962A pdb=" N ILE B 490 " --> pdb=" O HIS B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 523 removed outlier: 3.642A pdb=" N GLN B 513 " --> pdb=" O GLY B 509 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG B 514 " --> pdb=" O GLY B 510 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 523 " --> pdb=" O ARG B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 551 removed outlier: 3.874A pdb=" N LYS B 543 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU B 544 " --> pdb=" O GLU B 540 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 571 removed outlier: 3.503A pdb=" N ILE B 568 " --> pdb=" O ARG B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 593 Processing helix chain 'B' and resid 598 through 605 Processing helix chain 'B' and resid 608 through 613 removed outlier: 4.327A pdb=" N GLU B 612 " --> pdb=" O GLU B 608 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR B 613 " --> pdb=" O ALA B 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 608 through 613' Processing helix chain 'B' and resid 682 through 692 removed outlier: 3.745A pdb=" N TRP B 687 " --> pdb=" O ALA B 683 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET B 692 " --> pdb=" O ARG B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 712 removed outlier: 4.178A pdb=" N ILE B 709 " --> pdb=" O VAL B 705 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N CYS B 710 " --> pdb=" O GLY B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 728 removed outlier: 3.804A pdb=" N LEU B 725 " --> pdb=" O LEU B 721 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 726 " --> pdb=" O SER B 722 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 750 removed outlier: 4.568A pdb=" N LYS B 742 " --> pdb=" O LYS B 738 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR B 745 " --> pdb=" O ASP B 741 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE B 748 " --> pdb=" O CYS B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 763 removed outlier: 4.034A pdb=" N HIS B 762 " --> pdb=" O ASN B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 778 removed outlier: 3.835A pdb=" N VAL B 768 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY B 769 " --> pdb=" O TRP B 765 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS B 774 " --> pdb=" O GLU B 770 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 778 " --> pdb=" O LYS B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 787 removed outlier: 3.518A pdb=" N LYS B 786 " --> pdb=" O ALA B 783 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 787 " --> pdb=" O VAL B 784 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 783 through 787' Processing helix chain 'B' and resid 788 through 794 removed outlier: 3.894A pdb=" N ASP B 793 " --> pdb=" O ALA B 790 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN B 794 " --> pdb=" O TRP B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 806 removed outlier: 3.664A pdb=" N ALA B 803 " --> pdb=" O SER B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 818 removed outlier: 3.531A pdb=" N ARG B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 815 " --> pdb=" O ASN B 811 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 816 " --> pdb=" O ASN B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 825 removed outlier: 3.704A pdb=" N VAL B 825 " --> pdb=" O ILE B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 838 removed outlier: 3.898A pdb=" N MET B 831 " --> pdb=" O ASN B 827 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 834 " --> pdb=" O LEU B 830 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR B 836 " --> pdb=" O LEU B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 849 removed outlier: 3.965A pdb=" N VAL B 848 " --> pdb=" O ARG B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 867 removed outlier: 4.182A pdb=" N ALA B 859 " --> pdb=" O VAL B 855 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU B 862 " --> pdb=" O ALA B 858 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N MET B 867 " --> pdb=" O GLN B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 878 removed outlier: 4.245A pdb=" N HIS B 878 " --> pdb=" O LEU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 890 removed outlier: 3.565A pdb=" N ILE B 889 " --> pdb=" O ALA B 885 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 890 " --> pdb=" O GLY B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 898 removed outlier: 3.954A pdb=" N PHE B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 911 removed outlier: 3.786A pdb=" N ARG B 906 " --> pdb=" O ALA B 902 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B 908 " --> pdb=" O ILE B 904 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 910 " --> pdb=" O ARG B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 920 Processing helix chain 'B' and resid 931 through 939 removed outlier: 4.273A pdb=" N LEU B 937 " --> pdb=" O ALA B 933 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR B 938 " --> pdb=" O GLN B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 953 removed outlier: 3.618A pdb=" N SER B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS B 953 " --> pdb=" O SER B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 963 Processing helix chain 'B' and resid 965 through 971 Processing helix chain 'B' and resid 972 through 974 No H-bonds generated for 'chain 'B' and resid 972 through 974' Processing helix chain 'B' and resid 975 through 980 Processing helix chain 'B' and resid 981 through 986 Proline residue: B 984 - end of helix No H-bonds generated for 'chain 'B' and resid 981 through 986' Processing helix chain 'B' and resid 987 through 1000 removed outlier: 3.824A pdb=" N GLN B 991 " --> pdb=" O ILE B 987 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET B 993 " --> pdb=" O GLY B 989 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 999 " --> pdb=" O SER B 995 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B1000 " --> pdb=" O VAL B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1068 through 1073 Processing helix chain 'B' and resid 1094 through 1099 removed outlier: 3.593A pdb=" N ARG B1099 " --> pdb=" O LEU B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1115 through 1122 Processing helix chain 'B' and resid 1128 through 1139 removed outlier: 3.542A pdb=" N THR B1137 " --> pdb=" O ILE B1133 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA B1139 " --> pdb=" O ALA B1135 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.656A pdb=" N ALA B1147 " --> pdb=" O LYS B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1167 removed outlier: 3.613A pdb=" N GLN B1167 " --> pdb=" O SER B1164 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1164 through 1167' Processing helix chain 'B' and resid 1168 through 1178 removed outlier: 3.648A pdb=" N ALA B1172 " --> pdb=" O LYS B1168 " (cutoff:3.500A) Processing helix chain 'B' and resid 1194 through 1209 removed outlier: 3.951A pdb=" N ARG B1199 " --> pdb=" O ALA B1195 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER B1200 " --> pdb=" O GLU B1196 " (cutoff:3.500A) Processing helix chain 'B' and resid 1221 through 1227 removed outlier: 3.643A pdb=" N ILE B1224 " --> pdb=" O LEU B1221 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASN B1226 " --> pdb=" O THR B1223 " (cutoff:3.500A) Processing helix chain 'B' and resid 1243 through 1249 removed outlier: 4.032A pdb=" N LEU B1247 " --> pdb=" O SER B1243 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU B1248 " --> pdb=" O HIS B1244 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS B1249 " --> pdb=" O SER B1245 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1243 through 1249' Processing helix chain 'B' and resid 1254 through 1263 removed outlier: 3.567A pdb=" N ILE B1260 " --> pdb=" O TYR B1256 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN B1261 " --> pdb=" O ALA B1257 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B1262 " --> pdb=" O ARG B1258 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 389 through 391 removed outlier: 5.514A pdb=" N PHE B 389 " --> pdb=" O ASN B 372 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 369 " --> pdb=" O LEU B 428 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 560 through 561 removed outlier: 3.513A pdb=" N LEU B 401 " --> pdb=" O ILE B 560 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 400 " --> pdb=" O ALA B 575 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU B 577 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 576 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLU B 584 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 448 through 449 removed outlier: 4.140A pdb=" N VAL B 449 " --> pdb=" O LEU B 529 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 1046 through 1049 removed outlier: 3.742A pdb=" N ALA B1049 " --> pdb=" O VAL B1024 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B1024 " --> pdb=" O ALA B1049 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1214 through 1216 removed outlier: 6.502A pdb=" N THR B1054 " --> pdb=" O VAL B1229 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 771 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: 0.93 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2960 1.34 - 1.46: 1763 1.46 - 1.58: 4434 1.58 - 1.70: 4 1.70 - 1.82: 72 Bond restraints: 9233 Sorted by residual: bond pdb=" CB PRO B 394 " pdb=" CG PRO B 394 " ideal model delta sigma weight residual 1.492 1.670 -0.178 5.00e-02 4.00e+02 1.27e+01 bond pdb=" N PRO B 394 " pdb=" CA PRO B 394 " ideal model delta sigma weight residual 1.469 1.442 0.027 1.28e-02 6.10e+03 4.47e+00 bond pdb=" CB PRO B1034 " pdb=" CG PRO B1034 " ideal model delta sigma weight residual 1.492 1.595 -0.103 5.00e-02 4.00e+02 4.26e+00 bond pdb=" CG PRO B 394 " pdb=" CD PRO B 394 " ideal model delta sigma weight residual 1.503 1.433 0.070 3.40e-02 8.65e+02 4.22e+00 bond pdb=" CB GLN B 220 " pdb=" CG GLN B 220 " ideal model delta sigma weight residual 1.520 1.581 -0.061 3.00e-02 1.11e+03 4.10e+00 ... (remaining 9228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 12393 3.27 - 6.54: 80 6.54 - 9.81: 17 9.81 - 13.07: 4 13.07 - 16.34: 2 Bond angle restraints: 12496 Sorted by residual: angle pdb=" CA PRO B 394 " pdb=" N PRO B 394 " pdb=" CD PRO B 394 " ideal model delta sigma weight residual 112.00 95.66 16.34 1.40e+00 5.10e-01 1.36e+02 angle pdb=" CA PRO B1034 " pdb=" N PRO B1034 " pdb=" CD PRO B1034 " ideal model delta sigma weight residual 112.00 103.30 8.70 1.40e+00 5.10e-01 3.86e+01 angle pdb=" CA PRO B 695 " pdb=" N PRO B 695 " pdb=" CD PRO B 695 " ideal model delta sigma weight residual 112.00 104.22 7.78 1.40e+00 5.10e-01 3.09e+01 angle pdb=" N ILE B 925 " pdb=" CA ILE B 925 " pdb=" C ILE B 925 " ideal model delta sigma weight residual 113.43 107.54 5.89 1.09e+00 8.42e-01 2.92e+01 angle pdb=" N PRO B 394 " pdb=" CD PRO B 394 " pdb=" CG PRO B 394 " ideal model delta sigma weight residual 103.20 95.65 7.55 1.50e+00 4.44e-01 2.54e+01 ... (remaining 12491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 5033 18.01 - 36.01: 387 36.01 - 54.02: 83 54.02 - 72.03: 14 72.03 - 90.04: 4 Dihedral angle restraints: 5521 sinusoidal: 2127 harmonic: 3394 Sorted by residual: dihedral pdb=" CA PHE B 243 " pdb=" C PHE B 243 " pdb=" N VAL B 244 " pdb=" CA VAL B 244 " ideal model delta harmonic sigma weight residual -180.00 -142.78 -37.22 0 5.00e+00 4.00e-02 5.54e+01 dihedral pdb=" CA ILE B1072 " pdb=" C ILE B1072 " pdb=" N GLN B1073 " pdb=" CA GLN B1073 " ideal model delta harmonic sigma weight residual 180.00 157.39 22.61 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ALA B 533 " pdb=" C ALA B 533 " pdb=" N THR B 534 " pdb=" CA THR B 534 " ideal model delta harmonic sigma weight residual 180.00 159.85 20.15 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 5518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 944 0.043 - 0.085: 420 0.085 - 0.128: 68 0.128 - 0.170: 6 0.170 - 0.213: 6 Chirality restraints: 1444 Sorted by residual: chirality pdb=" CA PRO B 394 " pdb=" N PRO B 394 " pdb=" C PRO B 394 " pdb=" CB PRO B 394 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA PRO B 695 " pdb=" N PRO B 695 " pdb=" C PRO B 695 " pdb=" CB PRO B 695 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE B 527 " pdb=" CA ILE B 527 " pdb=" CG1 ILE B 527 " pdb=" CG2 ILE B 527 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 1441 not shown) Planarity restraints: 1587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B1033 " 0.086 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO B1034 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO B1034 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO B1034 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 694 " -0.069 5.00e-02 4.00e+02 1.00e-01 1.62e+01 pdb=" N PRO B 695 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO B 695 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 695 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 393 " 0.071 5.00e-02 4.00e+02 9.61e-02 1.48e+01 pdb=" N PRO B 394 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO B 394 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 394 " 0.053 5.00e-02 4.00e+02 ... (remaining 1584 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 46 2.52 - 3.12: 6652 3.12 - 3.71: 12969 3.71 - 4.31: 18238 4.31 - 4.90: 30141 Nonbonded interactions: 68046 Sorted by model distance: nonbonded pdb=" CE2 PHE B1144 " pdb=" OE1 GLN B1167 " model vdw 1.929 3.340 nonbonded pdb=" O VAL B 727 " pdb=" CE MET B 736 " model vdw 2.142 3.460 nonbonded pdb=" CZ PHE B1144 " pdb=" OE1 GLN B1167 " model vdw 2.157 3.340 nonbonded pdb=" O TRP B 791 " pdb=" ND2 ASN B 797 " model vdw 2.187 3.120 nonbonded pdb=" O LEU B 808 " pdb=" OD1 ASP B 809 " model vdw 2.212 3.040 ... (remaining 68041 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: 1.160 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.460 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.178 9233 Z= 0.209 Angle : 0.825 16.343 12496 Z= 0.463 Chirality : 0.045 0.213 1444 Planarity : 0.006 0.124 1587 Dihedral : 13.742 90.035 3337 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 0.00 % Allowed : 13.47 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.46 (0.21), residues: 1174 helix: -3.22 (0.16), residues: 682 sheet: -3.17 (0.66), residues: 55 loop : -2.12 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 117 TYR 0.018 0.001 TYR B 253 PHE 0.017 0.001 PHE B 72 TRP 0.021 0.002 TRP B 697 HIS 0.009 0.001 HIS B1228 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 9233) covalent geometry : angle 0.82474 (12496) hydrogen bonds : bond 0.26033 ( 272) hydrogen bonds : angle 8.75777 ( 771) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.225 Fit side-chains REVERT: B 434 LEU cc_start: 0.7759 (pp) cc_final: 0.7543 (pp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0712 time to fit residues: 10.3293 Evaluate side-chains 92 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 811 ASN ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN B1167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.214710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.161628 restraints weight = 10855.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.160051 restraints weight = 8989.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.161459 restraints weight = 8980.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.161548 restraints weight = 5909.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.161774 restraints weight = 5237.399| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 9233 Z= 0.139 Angle : 0.614 10.289 12496 Z= 0.319 Chirality : 0.042 0.167 1444 Planarity : 0.004 0.075 1587 Dihedral : 5.364 36.554 1266 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.51 % Allowed : 12.73 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.06 (0.22), residues: 1174 helix: -2.75 (0.17), residues: 684 sheet: -3.31 (0.53), residues: 72 loop : -2.08 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 117 TYR 0.016 0.001 TYR B1155 PHE 0.020 0.001 PHE B1144 TRP 0.012 0.001 TRP B 697 HIS 0.006 0.001 HIS B1228 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9233) covalent geometry : angle 0.61376 (12496) hydrogen bonds : bond 0.04499 ( 272) hydrogen bonds : angle 5.51933 ( 771) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.277 Fit side-chains REVERT: B 145 SER cc_start: 0.8563 (t) cc_final: 0.8268 (m) REVERT: B 1084 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.7189 (ptm) REVERT: B 1098 ILE cc_start: 0.9037 (tp) cc_final: 0.8575 (tp) outliers start: 24 outliers final: 10 residues processed: 122 average time/residue: 0.0534 time to fit residues: 9.9770 Evaluate side-chains 107 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 981 THR Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1137 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 50 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN B 303 ASN ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 811 ASN ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.214713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.162102 restraints weight = 10913.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.158486 restraints weight = 10969.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.160067 restraints weight = 9791.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.160499 restraints weight = 6267.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.160555 restraints weight = 6001.599| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9233 Z= 0.137 Angle : 0.593 9.685 12496 Z= 0.305 Chirality : 0.042 0.150 1444 Planarity : 0.004 0.063 1587 Dihedral : 5.195 36.769 1266 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.40 % Allowed : 13.47 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.75 (0.23), residues: 1174 helix: -2.55 (0.18), residues: 686 sheet: -3.24 (0.54), residues: 72 loop : -1.82 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 481 TYR 0.014 0.001 TYR B 253 PHE 0.018 0.001 PHE B 686 TRP 0.010 0.001 TRP B 946 HIS 0.005 0.001 HIS B1228 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9233) covalent geometry : angle 0.59286 (12496) hydrogen bonds : bond 0.03733 ( 272) hydrogen bonds : angle 5.10041 ( 771) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.231 Fit side-chains REVERT: B 145 SER cc_start: 0.8504 (t) cc_final: 0.8184 (m) REVERT: B 696 GLU cc_start: 0.7754 (pp20) cc_final: 0.7506 (pp20) REVERT: B 1098 ILE cc_start: 0.9135 (tp) cc_final: 0.8685 (tp) outliers start: 23 outliers final: 14 residues processed: 116 average time/residue: 0.0629 time to fit residues: 10.9037 Evaluate side-chains 106 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 981 THR Chi-restraints excluded: chain B residue 1054 THR Chi-restraints excluded: chain B residue 1137 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 10.0000 chunk 46 optimal weight: 0.0770 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 ASN ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 811 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.212376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.159504 restraints weight = 11051.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.153446 restraints weight = 9612.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.155271 restraints weight = 9975.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.156021 restraints weight = 6134.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.156389 restraints weight = 5476.575| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9233 Z= 0.163 Angle : 0.610 14.225 12496 Z= 0.310 Chirality : 0.043 0.164 1444 Planarity : 0.004 0.057 1587 Dihedral : 5.208 37.499 1266 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.34 % Allowed : 13.15 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.68 (0.23), residues: 1174 helix: -2.47 (0.18), residues: 690 sheet: -3.38 (0.54), residues: 74 loop : -1.79 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 117 TYR 0.015 0.001 TYR B 253 PHE 0.015 0.001 PHE B 72 TRP 0.010 0.001 TRP B 946 HIS 0.005 0.001 HIS B1228 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9233) covalent geometry : angle 0.60959 (12496) hydrogen bonds : bond 0.03625 ( 272) hydrogen bonds : angle 5.02040 ( 771) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.220 Fit side-chains REVERT: B 145 SER cc_start: 0.8525 (t) cc_final: 0.8187 (m) REVERT: B 434 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7830 (pp) REVERT: B 527 ILE cc_start: 0.8666 (mm) cc_final: 0.8464 (mm) REVERT: B 606 MET cc_start: 0.7768 (pmm) cc_final: 0.7535 (pmm) REVERT: B 696 GLU cc_start: 0.7766 (pp20) cc_final: 0.7471 (pp20) REVERT: B 865 MET cc_start: 0.7885 (mtm) cc_final: 0.7576 (mtm) REVERT: B 1098 ILE cc_start: 0.9156 (tp) cc_final: 0.8741 (tp) REVERT: B 1207 GLN cc_start: 0.7872 (tp-100) cc_final: 0.7601 (tp40) REVERT: B 1228 HIS cc_start: 0.5750 (t70) cc_final: 0.5542 (t-90) outliers start: 32 outliers final: 18 residues processed: 125 average time/residue: 0.0542 time to fit residues: 10.3275 Evaluate side-chains 111 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 981 THR Chi-restraints excluded: chain B residue 1071 LEU Chi-restraints excluded: chain B residue 1137 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.0270 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 ASN ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 811 ASN B1167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.215676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.163629 restraints weight = 10982.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.158758 restraints weight = 10882.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.160765 restraints weight = 10547.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.161113 restraints weight = 6209.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.161411 restraints weight = 5527.132| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9233 Z= 0.100 Angle : 0.569 9.953 12496 Z= 0.288 Chirality : 0.040 0.133 1444 Planarity : 0.004 0.053 1587 Dihedral : 4.878 35.692 1266 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.82 % Allowed : 15.14 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.38 (0.23), residues: 1174 helix: -2.20 (0.19), residues: 687 sheet: -3.31 (0.54), residues: 74 loop : -1.73 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 481 TYR 0.007 0.001 TYR B 253 PHE 0.009 0.001 PHE B 686 TRP 0.012 0.001 TRP B 946 HIS 0.005 0.001 HIS B1228 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 9233) covalent geometry : angle 0.56908 (12496) hydrogen bonds : bond 0.02909 ( 272) hydrogen bonds : angle 4.65058 ( 771) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.195 Fit side-chains REVERT: B 145 SER cc_start: 0.8444 (t) cc_final: 0.8095 (m) REVERT: B 808 LEU cc_start: 0.8415 (tt) cc_final: 0.8185 (tt) REVERT: B 811 ASN cc_start: 0.7610 (OUTLIER) cc_final: 0.7370 (m110) REVERT: B 865 MET cc_start: 0.7769 (mtm) cc_final: 0.7489 (mtm) REVERT: B 1098 ILE cc_start: 0.9166 (tp) cc_final: 0.8738 (tp) outliers start: 27 outliers final: 16 residues processed: 115 average time/residue: 0.0553 time to fit residues: 9.6680 Evaluate side-chains 105 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 728 TYR Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 811 ASN Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 981 THR Chi-restraints excluded: chain B residue 1071 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 11 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 ASN ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 811 ASN B1167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.177110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105998 restraints weight = 11160.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.108755 restraints weight = 6884.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110574 restraints weight = 5085.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.111496 restraints weight = 4265.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.112233 restraints weight = 3852.272| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9233 Z= 0.210 Angle : 0.652 9.658 12496 Z= 0.331 Chirality : 0.045 0.142 1444 Planarity : 0.004 0.052 1587 Dihedral : 5.196 37.863 1266 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.34 % Allowed : 16.08 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.52 (0.23), residues: 1174 helix: -2.31 (0.18), residues: 695 sheet: -3.29 (0.55), residues: 71 loop : -1.80 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 117 TYR 0.017 0.002 TYR B1117 PHE 0.019 0.002 PHE B 72 TRP 0.008 0.001 TRP B 946 HIS 0.004 0.001 HIS B1142 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 9233) covalent geometry : angle 0.65243 (12496) hydrogen bonds : bond 0.03733 ( 272) hydrogen bonds : angle 4.96525 ( 771) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.241 Fit side-chains REVERT: B 145 SER cc_start: 0.8570 (t) cc_final: 0.8200 (m) REVERT: B 808 LEU cc_start: 0.8735 (tt) cc_final: 0.8459 (tt) REVERT: B 811 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.7948 (m110) REVERT: B 865 MET cc_start: 0.7871 (mtm) cc_final: 0.7533 (mtm) REVERT: B 1098 ILE cc_start: 0.8848 (tp) cc_final: 0.8496 (tp) REVERT: B 1228 HIS cc_start: 0.5693 (t70) cc_final: 0.5286 (t-90) outliers start: 32 outliers final: 22 residues processed: 124 average time/residue: 0.0583 time to fit residues: 11.0101 Evaluate side-chains 118 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 811 ASN Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 873 ASP Chi-restraints excluded: chain B residue 901 GLU Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 981 THR Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1071 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 811 ASN B1167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.177634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.109359 restraints weight = 11080.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.111111 restraints weight = 7145.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.111491 restraints weight = 5459.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.111591 restraints weight = 4546.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.111883 restraints weight = 4445.175| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9233 Z= 0.147 Angle : 0.616 11.053 12496 Z= 0.309 Chirality : 0.043 0.234 1444 Planarity : 0.004 0.050 1587 Dihedral : 5.076 37.781 1266 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.61 % Allowed : 17.43 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.44 (0.23), residues: 1174 helix: -2.25 (0.18), residues: 697 sheet: -3.46 (0.55), residues: 67 loop : -1.73 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 481 TYR 0.012 0.001 TYR B 253 PHE 0.012 0.001 PHE B 72 TRP 0.011 0.001 TRP B 946 HIS 0.004 0.001 HIS B1142 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9233) covalent geometry : angle 0.61607 (12496) hydrogen bonds : bond 0.03319 ( 272) hydrogen bonds : angle 4.81684 ( 771) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.354 Fit side-chains REVERT: B 145 SER cc_start: 0.8558 (t) cc_final: 0.8183 (m) REVERT: B 808 LEU cc_start: 0.8742 (tt) cc_final: 0.8483 (tt) REVERT: B 811 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.7890 (t0) REVERT: B 865 MET cc_start: 0.7801 (mtm) cc_final: 0.7473 (mtm) REVERT: B 1098 ILE cc_start: 0.8866 (tp) cc_final: 0.8536 (tp) REVERT: B 1228 HIS cc_start: 0.5833 (t70) cc_final: 0.5456 (t-90) outliers start: 25 outliers final: 20 residues processed: 119 average time/residue: 0.0848 time to fit residues: 15.0901 Evaluate side-chains 115 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 811 ASN Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 873 ASP Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 953 LYS Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 981 THR Chi-restraints excluded: chain B residue 1024 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 86 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 65 optimal weight: 0.3980 chunk 89 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 303 ASN ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 811 ASN B1167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.178686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123029 restraints weight = 11119.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.116862 restraints weight = 14973.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.119124 restraints weight = 15659.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.119309 restraints weight = 8857.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.123074 restraints weight = 7462.055| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9233 Z= 0.135 Angle : 0.618 12.833 12496 Z= 0.308 Chirality : 0.043 0.212 1444 Planarity : 0.004 0.048 1587 Dihedral : 5.004 37.896 1266 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.71 % Allowed : 17.54 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.37 (0.23), residues: 1174 helix: -2.17 (0.18), residues: 697 sheet: -3.38 (0.54), residues: 74 loop : -1.71 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 481 TYR 0.011 0.001 TYR B 253 PHE 0.012 0.001 PHE B 72 TRP 0.011 0.001 TRP B 946 HIS 0.005 0.001 HIS B1142 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9233) covalent geometry : angle 0.61751 (12496) hydrogen bonds : bond 0.03198 ( 272) hydrogen bonds : angle 4.74800 ( 771) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.367 Fit side-chains REVERT: B 145 SER cc_start: 0.8474 (t) cc_final: 0.8106 (m) REVERT: B 606 MET cc_start: 0.7791 (pmm) cc_final: 0.7521 (pmm) REVERT: B 808 LEU cc_start: 0.8639 (tt) cc_final: 0.8390 (tt) REVERT: B 865 MET cc_start: 0.7849 (mtm) cc_final: 0.7519 (mtm) REVERT: B 1098 ILE cc_start: 0.9133 (tp) cc_final: 0.8722 (tp) REVERT: B 1102 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8507 (tt) REVERT: B 1228 HIS cc_start: 0.6073 (t70) cc_final: 0.5782 (t-90) outliers start: 26 outliers final: 22 residues processed: 121 average time/residue: 0.0844 time to fit residues: 15.2817 Evaluate side-chains 117 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 811 ASN Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 873 ASP Chi-restraints excluded: chain B residue 901 GLU Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 953 LYS Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 981 THR Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1102 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 38 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 30 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 303 ASN ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 811 ASN B1167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.177005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.106792 restraints weight = 11004.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.109608 restraints weight = 6729.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.111441 restraints weight = 4945.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.112505 restraints weight = 4114.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.113170 restraints weight = 3691.596| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9233 Z= 0.181 Angle : 0.652 12.340 12496 Z= 0.326 Chirality : 0.044 0.233 1444 Planarity : 0.004 0.047 1587 Dihedral : 5.127 37.763 1266 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.51 % Allowed : 17.95 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.37 (0.23), residues: 1174 helix: -2.20 (0.18), residues: 697 sheet: -3.35 (0.60), residues: 57 loop : -1.75 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 481 TYR 0.014 0.001 TYR B 253 PHE 0.015 0.001 PHE B 72 TRP 0.009 0.001 TRP B 946 HIS 0.005 0.001 HIS B1142 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 9233) covalent geometry : angle 0.65199 (12496) hydrogen bonds : bond 0.03497 ( 272) hydrogen bonds : angle 4.86991 ( 771) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.384 Fit side-chains REVERT: B 145 SER cc_start: 0.8525 (t) cc_final: 0.8152 (m) REVERT: B 606 MET cc_start: 0.8170 (pmm) cc_final: 0.7759 (pmm) REVERT: B 808 LEU cc_start: 0.8709 (tt) cc_final: 0.8417 (tt) REVERT: B 865 MET cc_start: 0.7856 (mtm) cc_final: 0.7515 (mtm) REVERT: B 1098 ILE cc_start: 0.8880 (tp) cc_final: 0.8514 (tp) REVERT: B 1102 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8182 (tt) REVERT: B 1228 HIS cc_start: 0.6007 (t70) cc_final: 0.5597 (t-90) outliers start: 24 outliers final: 21 residues processed: 116 average time/residue: 0.0817 time to fit residues: 14.3855 Evaluate side-chains 119 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 811 ASN Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 873 ASP Chi-restraints excluded: chain B residue 901 GLU Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 981 THR Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1102 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 65 optimal weight: 0.0170 chunk 102 optimal weight: 0.2980 chunk 84 optimal weight: 0.0870 chunk 69 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 98 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 811 ASN B1167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.180658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125374 restraints weight = 11015.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118679 restraints weight = 13875.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.120527 restraints weight = 14080.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.121958 restraints weight = 7930.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.122409 restraints weight = 6769.506| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9233 Z= 0.101 Angle : 0.607 11.776 12496 Z= 0.303 Chirality : 0.041 0.232 1444 Planarity : 0.004 0.047 1587 Dihedral : 4.794 35.763 1266 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.19 % Allowed : 17.95 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.08 (0.24), residues: 1174 helix: -1.96 (0.19), residues: 693 sheet: -3.15 (0.63), residues: 55 loop : -1.69 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 481 TYR 0.019 0.001 TYR B1117 PHE 0.006 0.001 PHE B 716 TRP 0.014 0.001 TRP B 946 HIS 0.005 0.001 HIS B1142 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 9233) covalent geometry : angle 0.60710 (12496) hydrogen bonds : bond 0.02786 ( 272) hydrogen bonds : angle 4.54172 ( 771) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.431 Fit side-chains REVERT: B 83 MET cc_start: 0.7311 (mtp) cc_final: 0.7076 (mtm) REVERT: B 145 SER cc_start: 0.8510 (t) cc_final: 0.8128 (m) REVERT: B 606 MET cc_start: 0.7874 (pmm) cc_final: 0.7593 (pmm) REVERT: B 808 LEU cc_start: 0.8589 (tt) cc_final: 0.8283 (tt) REVERT: B 811 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7910 (m110) REVERT: B 865 MET cc_start: 0.7809 (mtm) cc_final: 0.7517 (mtm) REVERT: B 978 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7287 (tm-30) REVERT: B 1098 ILE cc_start: 0.9058 (tp) cc_final: 0.8679 (tp) REVERT: B 1102 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8343 (tt) outliers start: 21 outliers final: 18 residues processed: 111 average time/residue: 0.0850 time to fit residues: 14.0808 Evaluate side-chains 113 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 736 MET Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 811 ASN Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 873 ASP Chi-restraints excluded: chain B residue 901 GLU Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 953 LYS Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 981 THR Chi-restraints excluded: chain B residue 1102 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 74 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 45 optimal weight: 0.0050 chunk 37 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 95 optimal weight: 9.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 303 ASN ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 811 ASN B1167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.180486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.124492 restraints weight = 10826.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.117858 restraints weight = 12514.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.119732 restraints weight = 12958.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.120135 restraints weight = 7846.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.120704 restraints weight = 7060.762| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 9233 Z= 0.107 Angle : 0.607 11.500 12496 Z= 0.303 Chirality : 0.041 0.229 1444 Planarity : 0.004 0.045 1587 Dihedral : 4.704 34.759 1266 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.40 % Allowed : 17.64 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.94 (0.24), residues: 1174 helix: -1.82 (0.19), residues: 687 sheet: -3.22 (0.61), residues: 55 loop : -1.68 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 481 TYR 0.008 0.001 TYR B 253 PHE 0.007 0.001 PHE B 72 TRP 0.011 0.001 TRP B 946 HIS 0.005 0.001 HIS B1142 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9233) covalent geometry : angle 0.60686 (12496) hydrogen bonds : bond 0.02785 ( 272) hydrogen bonds : angle 4.46647 ( 771) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1378.44 seconds wall clock time: 24 minutes 32.05 seconds (1472.05 seconds total)