Starting phenix.real_space_refine on Wed Apr 30 03:27:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpx_60366/04_2025/8zpx_60366.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpx_60366/04_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_60366/04_2025/8zpx_60366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpx_60366/04_2025/8zpx_60366.map" model { file = "/net/cci-nas-00/data/ceres_data/8zpx_60366/04_2025/8zpx_60366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpx_60366/04_2025/8zpx_60366.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.76, per 1000 atoms: 0.64 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.28 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: 3.21 Time building geometry restraints manager: 2.76 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: 0.770 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: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.000 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.260 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (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 TRP 0.021 0.002 TRP B 697 HIS 0.009 0.001 HIS B1228 PHE 0.017 0.001 PHE B 72 TYR 0.018 0.001 TYR B 253 ARG 0.005 0.000 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.26033 ( 272) hydrogen bonds : angle 8.75777 ( 771) covalent geometry : bond 0.00506 ( 9233) covalent geometry : angle 0.82474 (12496) *********************** 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 : 0.939 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: 0.2131 time to fit residues: 30.6505 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 : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 30 optimal weight: 0.2980 chunk 59 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 106 optimal weight: 5.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.4483 r_free = 0.4483 target = 0.215772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.162767 restraints weight = 10874.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.161910 restraints weight = 8844.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.162937 restraints weight = 8638.048| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9233 Z= 0.125 Angle : 0.604 10.051 12496 Z= 0.313 Chirality : 0.042 0.166 1444 Planarity : 0.004 0.074 1587 Dihedral : 5.299 35.981 1266 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.61 % Allowed : 12.53 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.22), residues: 1174 helix: -2.69 (0.17), residues: 679 sheet: -3.30 (0.53), residues: 72 loop : -2.02 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 697 HIS 0.005 0.001 HIS B1228 PHE 0.019 0.001 PHE B1144 TYR 0.016 0.001 TYR B1155 ARG 0.003 0.000 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 272) hydrogen bonds : angle 5.43995 ( 771) covalent geometry : bond 0.00289 ( 9233) covalent geometry : angle 0.60362 (12496) *********************** 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 129 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 1.067 Fit side-chains REVERT: B 145 SER cc_start: 0.8473 (t) cc_final: 0.8220 (m) REVERT: B 1098 ILE cc_start: 0.9093 (tp) cc_final: 0.8610 (tp) outliers start: 25 outliers final: 11 residues processed: 124 average time/residue: 0.1782 time to fit residues: 33.3500 Evaluate side-chains 105 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 1054 THR 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 51 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 14 optimal weight: 0.0020 chunk 33 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.5394 ------------------------------------------------------------------------------- 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 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 = 0.4444 r_free = 0.4444 target = 0.211529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.158605 restraints weight = 10985.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.154645 restraints weight = 10026.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.156674 restraints weight = 10519.716| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9233 Z= 0.186 Angle : 0.629 9.043 12496 Z= 0.323 Chirality : 0.044 0.148 1444 Planarity : 0.004 0.065 1587 Dihedral : 5.387 38.099 1266 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 3.03 % Allowed : 12.94 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.23), residues: 1174 helix: -2.62 (0.18), residues: 691 sheet: -3.28 (0.54), residues: 72 loop : -1.88 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 791 HIS 0.005 0.001 HIS B1228 PHE 0.018 0.002 PHE B 72 TYR 0.016 0.001 TYR B 253 ARG 0.004 0.000 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.04204 ( 272) hydrogen bonds : angle 5.28860 ( 771) covalent geometry : bond 0.00439 ( 9233) covalent geometry : angle 0.62868 (12496) *********************** 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 122 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 1.935 Fit side-chains REVERT: B 145 SER cc_start: 0.8574 (t) cc_final: 0.8254 (m) REVERT: B 696 GLU cc_start: 0.7886 (pp20) cc_final: 0.7410 (pp20) REVERT: B 865 MET cc_start: 0.7918 (mtm) cc_final: 0.7609 (mtm) REVERT: B 1098 ILE cc_start: 0.9166 (tp) cc_final: 0.8725 (tp) outliers start: 29 outliers final: 16 residues processed: 118 average time/residue: 0.2441 time to fit residues: 42.8618 Evaluate side-chains 106 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 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 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 1137 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 45 optimal weight: 6.9990 chunk 40 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4464 r_free = 0.4464 target = 0.213738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.160767 restraints weight = 10863.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.156336 restraints weight = 10715.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.158030 restraints weight = 9438.788| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9233 Z= 0.130 Angle : 0.589 14.036 12496 Z= 0.299 Chirality : 0.042 0.163 1444 Planarity : 0.004 0.058 1587 Dihedral : 5.140 37.089 1266 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.40 % Allowed : 13.88 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.23), residues: 1174 helix: -2.44 (0.18), residues: 693 sheet: -3.36 (0.54), residues: 74 loop : -1.75 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 946 HIS 0.005 0.001 HIS B1228 PHE 0.011 0.001 PHE B 72 TYR 0.013 0.001 TYR B1117 ARG 0.003 0.000 ARG B 481 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 272) hydrogen bonds : angle 4.94417 ( 771) covalent geometry : bond 0.00303 ( 9233) covalent geometry : angle 0.58883 (12496) *********************** 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 119 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 1.336 Fit side-chains REVERT: B 145 SER cc_start: 0.8576 (t) cc_final: 0.8236 (m) REVERT: B 606 MET cc_start: 0.7855 (pmm) cc_final: 0.7575 (pmm) REVERT: B 696 GLU cc_start: 0.8020 (pp20) cc_final: 0.7622 (pp20) REVERT: B 865 MET cc_start: 0.7851 (mtm) cc_final: 0.7531 (mtm) REVERT: B 1098 ILE cc_start: 0.9081 (tp) cc_final: 0.8692 (tp) REVERT: B 1207 GLN cc_start: 0.7974 (tp-100) cc_final: 0.7651 (tp40) REVERT: B 1228 HIS cc_start: 0.5776 (t70) cc_final: 0.5568 (t-90) outliers start: 23 outliers final: 13 residues processed: 114 average time/residue: 0.2216 time to fit residues: 38.8962 Evaluate side-chains 106 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 1071 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 104 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4477 r_free = 0.4477 target = 0.215316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.162725 restraints weight = 10907.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.159169 restraints weight = 10156.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.160985 restraints weight = 9797.754| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9233 Z= 0.106 Angle : 0.568 9.413 12496 Z= 0.288 Chirality : 0.041 0.136 1444 Planarity : 0.004 0.054 1587 Dihedral : 4.876 35.752 1266 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.13 % Allowed : 14.61 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.23), residues: 1174 helix: -2.18 (0.19), residues: 689 sheet: -3.30 (0.55), residues: 74 loop : -1.70 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 946 HIS 0.005 0.001 HIS B1228 PHE 0.008 0.001 PHE B 686 TYR 0.008 0.001 TYR B 253 ARG 0.004 0.000 ARG B 481 Details of bonding type rmsd hydrogen bonds : bond 0.02931 ( 272) hydrogen bonds : angle 4.64927 ( 771) covalent geometry : bond 0.00239 ( 9233) covalent geometry : angle 0.56760 (12496) *********************** 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 125 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.964 Fit side-chains REVERT: B 145 SER cc_start: 0.8477 (t) cc_final: 0.8122 (m) REVERT: B 808 LEU cc_start: 0.8387 (tt) cc_final: 0.8135 (tt) REVERT: B 811 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.7402 (m110) REVERT: B 865 MET cc_start: 0.7847 (mtm) cc_final: 0.7575 (mtm) REVERT: B 1098 ILE cc_start: 0.9175 (tp) cc_final: 0.8748 (tp) outliers start: 30 outliers final: 19 residues processed: 119 average time/residue: 0.1896 time to fit residues: 33.7409 Evaluate side-chains 111 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 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 873 ASP 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 39 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 115 optimal weight: 0.0040 chunk 76 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.181309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125626 restraints weight = 10887.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121560 restraints weight = 14596.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.123438 restraints weight = 15150.795| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9233 Z= 0.103 Angle : 0.581 10.253 12496 Z= 0.292 Chirality : 0.041 0.130 1444 Planarity : 0.004 0.050 1587 Dihedral : 4.762 34.738 1266 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.92 % Allowed : 15.55 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.24), residues: 1174 helix: -2.08 (0.19), residues: 694 sheet: -3.30 (0.54), residues: 74 loop : -1.60 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 946 HIS 0.005 0.001 HIS B1142 PHE 0.007 0.001 PHE B 72 TYR 0.017 0.001 TYR B1117 ARG 0.004 0.000 ARG B 481 Details of bonding type rmsd hydrogen bonds : bond 0.02821 ( 272) hydrogen bonds : angle 4.53935 ( 771) covalent geometry : bond 0.00237 ( 9233) covalent geometry : angle 0.58114 (12496) *********************** 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 124 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 1.106 Fit side-chains REVERT: B 145 SER cc_start: 0.8552 (t) cc_final: 0.8168 (m) REVERT: B 808 LEU cc_start: 0.8677 (tt) cc_final: 0.8383 (tt) REVERT: B 811 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7871 (m110) REVERT: B 865 MET cc_start: 0.7779 (mtm) cc_final: 0.7506 (mtm) REVERT: B 1055 LEU cc_start: 0.7627 (tt) cc_final: 0.7146 (mp) REVERT: B 1098 ILE cc_start: 0.9073 (tp) cc_final: 0.8697 (tp) REVERT: B 1228 HIS cc_start: 0.5932 (t70) cc_final: 0.5676 (t-90) outliers start: 28 outliers final: 20 residues processed: 120 average time/residue: 0.1822 time to fit residues: 32.8281 Evaluate side-chains 113 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 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 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 1071 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 79 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 0.0060 chunk 11 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.180344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.111624 restraints weight = 10862.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.114506 restraints weight = 6406.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.116449 restraints weight = 4626.836| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9233 Z= 0.111 Angle : 0.584 9.614 12496 Z= 0.293 Chirality : 0.041 0.225 1444 Planarity : 0.004 0.048 1587 Dihedral : 4.721 35.196 1266 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.13 % Allowed : 15.66 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.24), residues: 1174 helix: -1.98 (0.19), residues: 692 sheet: -3.27 (0.54), residues: 74 loop : -1.62 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 946 HIS 0.005 0.001 HIS B1142 PHE 0.009 0.001 PHE B 72 TYR 0.010 0.001 TYR B 253 ARG 0.004 0.000 ARG B 481 Details of bonding type rmsd hydrogen bonds : bond 0.02841 ( 272) hydrogen bonds : angle 4.50005 ( 771) covalent geometry : bond 0.00256 ( 9233) covalent geometry : angle 0.58360 (12496) *********************** 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 130 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.981 Fit side-chains REVERT: B 145 SER cc_start: 0.8461 (t) cc_final: 0.8081 (m) REVERT: B 808 LEU cc_start: 0.8642 (tt) cc_final: 0.8335 (tt) REVERT: B 865 MET cc_start: 0.7741 (mtm) cc_final: 0.7460 (mtm) REVERT: B 1055 LEU cc_start: 0.7170 (tt) cc_final: 0.6757 (mp) REVERT: B 1098 ILE cc_start: 0.8913 (tp) cc_final: 0.8533 (tp) REVERT: B 1228 HIS cc_start: 0.5770 (t70) cc_final: 0.5428 (t-90) outliers start: 30 outliers final: 23 residues processed: 124 average time/residue: 0.1813 time to fit residues: 33.3579 Evaluate side-chains 116 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 350 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 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 1071 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 0.0010 chunk 86 optimal weight: 0.4980 chunk 65 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 overall best weight: 0.3986 ------------------------------------------------------------------------------- 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 ** 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 = 0.4013 r_free = 0.4013 target = 0.181666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126837 restraints weight = 10866.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121405 restraints weight = 13245.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.123756 restraints weight = 14402.662| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9233 Z= 0.096 Angle : 0.579 9.349 12496 Z= 0.291 Chirality : 0.041 0.204 1444 Planarity : 0.003 0.047 1587 Dihedral : 4.579 32.968 1266 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.51 % Allowed : 17.12 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.24), residues: 1174 helix: -1.81 (0.19), residues: 687 sheet: -3.25 (0.54), residues: 74 loop : -1.66 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 946 HIS 0.005 0.001 HIS B1142 PHE 0.007 0.001 PHE B 375 TYR 0.006 0.001 TYR B 253 ARG 0.004 0.000 ARG B 481 Details of bonding type rmsd hydrogen bonds : bond 0.02620 ( 272) hydrogen bonds : angle 4.36409 ( 771) covalent geometry : bond 0.00215 ( 9233) covalent geometry : angle 0.57862 (12496) *********************** 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 119 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 1.063 Fit side-chains REVERT: B 220 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6807 (tm130) REVERT: B 808 LEU cc_start: 0.8655 (tt) cc_final: 0.8402 (tt) REVERT: B 865 MET cc_start: 0.7692 (mtm) cc_final: 0.7401 (mtm) REVERT: B 1055 LEU cc_start: 0.7617 (tt) cc_final: 0.7144 (mp) REVERT: B 1098 ILE cc_start: 0.9083 (tp) cc_final: 0.8703 (tp) REVERT: B 1228 HIS cc_start: 0.5914 (t70) cc_final: 0.5646 (t-90) outliers start: 24 outliers final: 20 residues processed: 113 average time/residue: 0.1817 time to fit residues: 31.0376 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 : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 350 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 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 1071 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 65 optimal weight: 0.0570 chunk 59 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 0.0970 chunk 57 optimal weight: 7.9990 chunk 82 optimal weight: 0.0000 chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.6102 ------------------------------------------------------------------------------- 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 ** 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 = 0.4023 r_free = 0.4023 target = 0.182628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.126072 restraints weight = 10884.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.119814 restraints weight = 13120.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.122188 restraints weight = 14252.087| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9233 Z= 0.108 Angle : 0.583 9.136 12496 Z= 0.293 Chirality : 0.041 0.200 1444 Planarity : 0.003 0.047 1587 Dihedral : 4.563 33.327 1266 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.61 % Allowed : 17.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.24), residues: 1174 helix: -1.74 (0.19), residues: 690 sheet: -3.26 (0.54), residues: 74 loop : -1.62 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 946 HIS 0.005 0.001 HIS B1142 PHE 0.007 0.001 PHE B 72 TYR 0.018 0.001 TYR B1117 ARG 0.004 0.000 ARG B 481 Details of bonding type rmsd hydrogen bonds : bond 0.02692 ( 272) hydrogen bonds : angle 4.33976 ( 771) covalent geometry : bond 0.00249 ( 9233) covalent geometry : angle 0.58302 (12496) *********************** 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 120 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.955 Fit side-chains REVERT: B 220 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6806 (tm130) REVERT: B 808 LEU cc_start: 0.8671 (tt) cc_final: 0.8417 (tt) REVERT: B 865 MET cc_start: 0.7688 (mtm) cc_final: 0.7401 (mtm) REVERT: B 1055 LEU cc_start: 0.7619 (tt) cc_final: 0.7140 (mp) REVERT: B 1098 ILE cc_start: 0.9061 (tp) cc_final: 0.8694 (tp) REVERT: B 1228 HIS cc_start: 0.5917 (t70) cc_final: 0.5636 (t-90) outliers start: 25 outliers final: 20 residues processed: 114 average time/residue: 0.1811 time to fit residues: 31.2194 Evaluate side-chains 113 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 350 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 873 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 15 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 0.0470 chunk 49 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.8080 ------------------------------------------------------------------------------- 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 ** 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 = 0.4198 r_free = 0.4198 target = 0.196233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.145289 restraints weight = 10731.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.140423 restraints weight = 15768.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.142552 restraints weight = 13814.900| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9233 Z= 0.121 Angle : 0.592 10.814 12496 Z= 0.296 Chirality : 0.042 0.198 1444 Planarity : 0.003 0.046 1587 Dihedral : 4.599 33.427 1266 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.19 % Allowed : 18.16 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.24), residues: 1174 helix: -1.72 (0.19), residues: 695 sheet: -3.18 (0.55), residues: 72 loop : -1.57 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 946 HIS 0.005 0.001 HIS B1142 PHE 0.009 0.001 PHE B 72 TYR 0.011 0.001 TYR B 253 ARG 0.004 0.000 ARG B 481 Details of bonding type rmsd hydrogen bonds : bond 0.02807 ( 272) hydrogen bonds : angle 4.36656 ( 771) covalent geometry : bond 0.00282 ( 9233) covalent geometry : angle 0.59185 (12496) ********************** 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 : 0.943 Fit side-chains REVERT: B 220 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6915 (tm-30) REVERT: B 808 LEU cc_start: 0.8720 (tt) cc_final: 0.8503 (tt) REVERT: B 865 MET cc_start: 0.7684 (mtm) cc_final: 0.7388 (mtm) REVERT: B 1055 LEU cc_start: 0.7750 (tt) cc_final: 0.7304 (mp) REVERT: B 1098 ILE cc_start: 0.9065 (tp) cc_final: 0.8685 (tp) outliers start: 21 outliers final: 20 residues processed: 109 average time/residue: 0.1731 time to fit residues: 28.4055 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 : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 350 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 873 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 89 optimal weight: 0.2980 chunk 44 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 5 optimal weight: 0.0470 chunk 110 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 0.0050 chunk 56 optimal weight: 9.9990 chunk 38 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 overall best weight: 0.7694 ------------------------------------------------------------------------------- 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 ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.181685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.125764 restraints weight = 10884.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.121659 restraints weight = 15140.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.123768 restraints weight = 15314.861| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9233 Z= 0.116 Angle : 0.590 10.131 12496 Z= 0.296 Chirality : 0.042 0.196 1444 Planarity : 0.003 0.047 1587 Dihedral : 4.601 33.721 1266 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.61 % Allowed : 18.16 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.24), residues: 1174 helix: -1.68 (0.19), residues: 696 sheet: -3.25 (0.58), residues: 66 loop : -1.54 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 946 HIS 0.006 0.001 HIS B1228 PHE 0.009 0.001 PHE B 72 TYR 0.010 0.001 TYR B 253 ARG 0.004 0.000 ARG B 481 Details of bonding type rmsd hydrogen bonds : bond 0.02803 ( 272) hydrogen bonds : angle 4.35659 ( 771) covalent geometry : bond 0.00272 ( 9233) covalent geometry : angle 0.59011 (12496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3280.07 seconds wall clock time: 59 minutes 49.97 seconds (3589.97 seconds total)