Starting phenix.real_space_refine on Sat Aug 23 03:01:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zq4_60370/08_2025/8zq4_60370.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zq4_60370/08_2025/8zq4_60370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zq4_60370/08_2025/8zq4_60370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zq4_60370/08_2025/8zq4_60370.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zq4_60370/08_2025/8zq4_60370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zq4_60370/08_2025/8zq4_60370.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 43 5.16 5 C 5874 2.51 5 N 1582 2.21 5 O 1711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9216 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 9120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1186, 9120 Classifications: {'peptide': 1186} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 31, 'TRANS': 1154} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Unusual residues: {'ATP': 2, 'BLD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.86, per 1000 atoms: 0.20 Number of scatterers: 9216 At special positions: 0 Unit cell: (71.5, 108.9, 145.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 P 6 15.00 O 1711 8.00 N 1582 7.00 C 5874 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 263.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 5 sheets defined 57.4% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'B' and resid 38 through 42 Processing helix chain 'B' and resid 45 through 54 removed outlier: 4.280A pdb=" N ALA B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 74 removed outlier: 3.703A pdb=" N LEU B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 63 " --> pdb=" O PRO B 59 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 90 removed outlier: 3.765A pdb=" N MET B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLU B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 99 removed outlier: 3.778A pdb=" N VAL B 96 " --> pdb=" O TYR B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 removed outlier: 3.924A pdb=" N LYS B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 127 " --> pdb=" O ARG B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 159 through 162 Processing helix chain 'B' and resid 163 through 179 removed outlier: 3.612A pdb=" N GLY B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 removed outlier: 3.718A pdb=" N THR B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 203 Processing helix chain 'B' and resid 204 through 226 removed outlier: 3.556A pdb=" N THR B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLN B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'B' and resid 250 through 256 removed outlier: 3.551A pdb=" N SER B 255 " --> pdb=" O GLN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.840A pdb=" N LYS B 262 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 277 removed outlier: 3.850A pdb=" N GLY B 268 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 269 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.668A pdb=" N CYS B 285 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.545A pdb=" N LEU B 296 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG B 298 " --> pdb=" O GLY B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 removed outlier: 3.543A pdb=" N MET B 315 " --> pdb=" O MET B 311 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 324 Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 331 through 338 removed outlier: 4.106A pdb=" N LYS B 335 " --> pdb=" O PHE B 331 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 346 removed outlier: 3.895A pdb=" N ASP B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 417 removed outlier: 4.009A pdb=" N ILE B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 412 through 417' Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 459 through 465 removed outlier: 3.548A pdb=" N ASN B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 483 removed outlier: 3.889A pdb=" N ILE B 476 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU B 478 " --> pdb=" O VAL B 474 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 479 " --> pdb=" O GLU B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 492 removed outlier: 3.649A pdb=" N ILE B 490 " --> pdb=" O HIS B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 498 Processing helix chain 'B' and resid 508 through 522 removed outlier: 3.694A pdb=" N ILE B 515 " --> pdb=" O GLN B 511 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B 516 " --> pdb=" O LYS B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 553 removed outlier: 3.855A pdb=" N LYS B 543 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG B 551 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 570 removed outlier: 3.621A pdb=" N ILE B 568 " --> pdb=" O ARG B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 594 Processing helix chain 'B' and resid 599 through 606 removed outlier: 3.527A pdb=" N LYS B 605 " --> pdb=" O ALA B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 624 removed outlier: 3.528A pdb=" N GLU B 612 " --> pdb=" O GLU B 608 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR B 613 " --> pdb=" O ALA B 609 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 614 " --> pdb=" O ALA B 610 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET B 615 " --> pdb=" O HIS B 611 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN B 617 " --> pdb=" O THR B 613 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 713 removed outlier: 3.662A pdb=" N CYS B 710 " --> pdb=" O GLY B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 728 removed outlier: 3.651A pdb=" N LEU B 725 " --> pdb=" O LEU B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 756 removed outlier: 3.782A pdb=" N LYS B 738 " --> pdb=" O GLU B 734 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N TYR B 743 " --> pdb=" O GLN B 739 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR B 745 " --> pdb=" O ASP B 741 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU B 747 " --> pdb=" O TYR B 743 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 751 " --> pdb=" O LEU B 747 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA B 753 " --> pdb=" O GLY B 749 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA B 754 " --> pdb=" O LEU B 750 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 755 " --> pdb=" O SER B 751 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 756 " --> pdb=" O SER B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 785 removed outlier: 4.239A pdb=" N GLY B 769 " --> pdb=" O TRP B 765 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN B 771 " --> pdb=" O ILE B 767 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 772 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG B 775 " --> pdb=" O ASN B 771 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS B 779 " --> pdb=" O ARG B 775 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 781 " --> pdb=" O ARG B 777 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER B 782 " --> pdb=" O GLU B 778 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 785 " --> pdb=" O LEU B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 793 removed outlier: 3.586A pdb=" N PHE B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP B 793 " --> pdb=" O MET B 789 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 788 through 793' Processing helix chain 'B' and resid 798 through 803 removed outlier: 3.513A pdb=" N ILE B 802 " --> pdb=" O GLU B 798 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA B 803 " --> pdb=" O SER B 799 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 798 through 803' Processing helix chain 'B' and resid 807 through 812 removed outlier: 3.587A pdb=" N ASN B 811 " --> pdb=" O ALA B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 818 removed outlier: 4.405A pdb=" N ILE B 817 " --> pdb=" O VAL B 813 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY B 818 " --> pdb=" O ARG B 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 813 through 818' Processing helix chain 'B' and resid 818 through 827 removed outlier: 3.948A pdb=" N SER B 822 " --> pdb=" O GLY B 818 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE B 824 " --> pdb=" O ARG B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 842 removed outlier: 4.178A pdb=" N THR B 836 " --> pdb=" O LEU B 832 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 837 " --> pdb=" O VAL B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 852 removed outlier: 4.157A pdb=" N VAL B 848 " --> pdb=" O ARG B 844 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL B 850 " --> pdb=" O ALA B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 866 removed outlier: 3.719A pdb=" N VAL B 857 " --> pdb=" O PHE B 853 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 863 " --> pdb=" O ALA B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 877 No H-bonds generated for 'chain 'B' and resid 875 through 877' Processing helix chain 'B' and resid 878 through 891 removed outlier: 3.582A pdb=" N THR B 882 " --> pdb=" O HIS B 878 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU B 884 " --> pdb=" O LYS B 880 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 885 " --> pdb=" O GLY B 881 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 889 " --> pdb=" O ALA B 885 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B 890 " --> pdb=" O GLY B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 898 removed outlier: 3.612A pdb=" N PHE B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 910 removed outlier: 3.833A pdb=" N ALA B 910 " --> pdb=" O ARG B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 922 removed outlier: 4.217A pdb=" N CYS B 919 " --> pdb=" O PRO B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 927 Processing helix chain 'B' and resid 927 through 932 Processing helix chain 'B' and resid 935 through 945 removed outlier: 3.694A pdb=" N SER B 940 " --> pdb=" O CYS B 936 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA B 942 " --> pdb=" O TYR B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 954 removed outlier: 3.773A pdb=" N LEU B 951 " --> pdb=" O TYR B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 981 removed outlier: 3.605A pdb=" N THR B 962 " --> pdb=" O ASP B 958 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B 964 " --> pdb=" O SER B 960 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET B 967 " --> pdb=" O ILE B 963 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 968 " --> pdb=" O ARG B 964 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA B 973 " --> pdb=" O LEU B 969 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA B 977 " --> pdb=" O ALA B 973 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR B 979 " --> pdb=" O GLY B 975 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU B 980 " --> pdb=" O ALA B 976 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR B 981 " --> pdb=" O ALA B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1001 removed outlier: 3.631A pdb=" N PHE B 997 " --> pdb=" O MET B 993 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 999 " --> pdb=" O SER B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1067 removed outlier: 4.254A pdb=" N GLY B1064 " --> pdb=" O SER B1061 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS B1065 " --> pdb=" O GLY B1062 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B1066 " --> pdb=" O CYS B1063 " (cutoff:3.500A) Processing helix chain 'B' and resid 1068 through 1073 removed outlier: 3.529A pdb=" N ILE B1072 " --> pdb=" O VAL B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1099 Processing helix chain 'B' and resid 1115 through 1122 Processing helix chain 'B' and resid 1128 through 1139 removed outlier: 3.640A pdb=" N ILE B1132 " --> pdb=" O THR B1128 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'B' and resid 1150 through 1154 Processing helix chain 'B' and resid 1164 through 1178 removed outlier: 4.082A pdb=" N VAL B1178 " --> pdb=" O ALA B1174 " (cutoff:3.500A) Processing helix chain 'B' and resid 1194 through 1208 removed outlier: 3.567A pdb=" N ARG B1199 " --> pdb=" O ALA B1195 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN B1207 " --> pdb=" O GLU B1203 " (cutoff:3.500A) Processing helix chain 'B' and resid 1243 through 1248 removed outlier: 3.522A pdb=" N LEU B1248 " --> pdb=" O HIS B1244 " (cutoff:3.500A) Processing helix chain 'B' and resid 1254 through 1263 removed outlier: 3.925A pdb=" N ARG B1258 " --> pdb=" O GLY B1254 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE B1260 " --> pdb=" O TYR B1256 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN B1261 " --> pdb=" O ALA B1257 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 386 through 393 removed outlier: 5.392A pdb=" N VAL B 373 " --> pdb=" O ASN B 388 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N CYS B 390 " --> pdb=" O LYS B 371 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LYS B 371 " --> pdb=" O CYS B 390 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N SER B 392 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLU B 369 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 446 through 449 removed outlier: 3.670A pdb=" N LEU B 401 " --> pdb=" O ILE B 560 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR B 398 " --> pdb=" O LEU B 573 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ALA B 575 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA B 400 " --> pdb=" O ALA B 575 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU B 577 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL B 574 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE B 585 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL B 576 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 1042 through 1048 removed outlier: 6.460A pdb=" N ARG B1043 " --> pdb=" O PHE B1031 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N PHE B1031 " --> pdb=" O ARG B1043 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU B1047 " --> pdb=" O LYS B1027 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LYS B1027 " --> pdb=" O LEU B1047 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE B1029 " --> pdb=" O SER B1080 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER B1080 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1057 through 1058 removed outlier: 3.960A pdb=" N VAL B1232 " --> pdb=" O GLU B1240 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU B1240 " --> pdb=" O VAL B1232 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASP B1234 " --> pdb=" O VAL B1238 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL B1238 " --> pdb=" O ASP B1234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1102 through 1104 309 hydrogen bonds defined for protein. 882 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1506 1.32 - 1.44: 2447 1.44 - 1.56: 5356 1.56 - 1.69: 10 1.69 - 1.81: 72 Bond restraints: 9391 Sorted by residual: bond pdb=" C4 ATP B1301 " pdb=" C5 ATP B1301 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.31e+01 bond pdb=" C4 ATP B1302 " pdb=" C5 ATP B1302 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.03e+01 bond pdb=" C5 ATP B1301 " pdb=" C6 ATP B1301 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.46e+01 bond pdb=" C5 ATP B1302 " pdb=" C6 ATP B1302 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.40e+01 bond pdb=" C8 ATP B1301 " pdb=" N7 ATP B1301 " ideal model delta sigma weight residual 1.310 1.355 -0.045 1.00e-02 1.00e+04 2.00e+01 ... (remaining 9386 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 12597 3.76 - 7.51: 118 7.51 - 11.27: 11 11.27 - 15.03: 4 15.03 - 18.78: 2 Bond angle restraints: 12732 Sorted by residual: angle pdb=" PB ATP B1301 " pdb=" O3B ATP B1301 " pdb=" PG ATP B1301 " ideal model delta sigma weight residual 139.87 121.09 18.78 1.00e+00 1.00e+00 3.53e+02 angle pdb=" PB ATP B1302 " pdb=" O3B ATP B1302 " pdb=" PG ATP B1302 " ideal model delta sigma weight residual 139.87 124.36 15.51 1.00e+00 1.00e+00 2.41e+02 angle pdb=" PA ATP B1302 " pdb=" O3A ATP B1302 " pdb=" PB ATP B1302 " ideal model delta sigma weight residual 136.83 122.97 13.86 1.00e+00 1.00e+00 1.92e+02 angle pdb=" PA ATP B1301 " pdb=" O3A ATP B1301 " pdb=" PB ATP B1301 " ideal model delta sigma weight residual 136.83 123.15 13.68 1.00e+00 1.00e+00 1.87e+02 angle pdb=" C5 ATP B1302 " pdb=" C4 ATP B1302 " pdb=" N3 ATP B1302 " ideal model delta sigma weight residual 126.80 118.87 7.93 1.00e+00 1.00e+00 6.29e+01 ... (remaining 12727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 5402 17.05 - 34.10: 238 34.10 - 51.15: 57 51.15 - 68.20: 7 68.20 - 85.25: 7 Dihedral angle restraints: 5711 sinusoidal: 2293 harmonic: 3418 Sorted by residual: dihedral pdb=" CA SER B 694 " pdb=" C SER B 694 " pdb=" N PRO B 695 " pdb=" CA PRO B 695 " ideal model delta harmonic sigma weight residual 180.00 144.49 35.51 0 5.00e+00 4.00e-02 5.04e+01 dihedral pdb=" CA THR B 185 " pdb=" C THR B 185 " pdb=" N ALA B 186 " pdb=" CA ALA B 186 " ideal model delta harmonic sigma weight residual 180.00 147.47 32.53 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA ILE B 100 " pdb=" C ILE B 100 " pdb=" N TRP B 101 " pdb=" CA TRP B 101 " ideal model delta harmonic sigma weight residual 180.00 149.25 30.75 0 5.00e+00 4.00e-02 3.78e+01 ... (remaining 5708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1070 0.058 - 0.115: 341 0.115 - 0.173: 49 0.173 - 0.230: 10 0.230 - 0.288: 2 Chirality restraints: 1472 Sorted by residual: chirality pdb=" CB ILE B 100 " pdb=" CA ILE B 100 " pdb=" CG1 ILE B 100 " pdb=" CG2 ILE B 100 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C10 BLD B1303 " pdb=" C01 BLD B1303 " pdb=" C05 BLD B1303 " pdb=" C09 BLD B1303 " both_signs ideal model delta sigma weight residual False -3.02 -2.78 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA PRO B 625 " pdb=" N PRO B 625 " pdb=" C PRO B 625 " pdb=" CB PRO B 625 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1469 not shown) Planarity restraints: 1601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 694 " -0.062 5.00e-02 4.00e+02 9.23e-02 1.36e+01 pdb=" N PRO B 695 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO B 695 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 695 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 913 " -0.058 5.00e-02 4.00e+02 8.72e-02 1.22e+01 pdb=" N PRO B 914 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 914 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 914 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 58 " -0.057 5.00e-02 4.00e+02 8.51e-02 1.16e+01 pdb=" N PRO B 59 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " -0.048 5.00e-02 4.00e+02 ... (remaining 1598 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2568 2.80 - 3.33: 7995 3.33 - 3.85: 14145 3.85 - 4.38: 16706 4.38 - 4.90: 27254 Nonbonded interactions: 68668 Sorted by model distance: nonbonded pdb=" O LYS B 165 " pdb=" OG SER B 327 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR B 377 " pdb=" OG1 THR B 411 " model vdw 2.314 3.040 nonbonded pdb=" OG1 THR B1014 " pdb=" O LYS B1092 " model vdw 2.314 3.040 nonbonded pdb=" OE1 GLU B 231 " pdb=" OG SER B 799 " model vdw 2.330 3.040 nonbonded pdb=" OH TYR B1117 " pdb=" OE1 GLU B1129 " model vdw 2.352 3.040 ... (remaining 68663 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.250 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.007 0.079 9392 Z= 0.360 Angle : 1.052 18.783 12732 Z= 0.652 Chirality : 0.055 0.288 1472 Planarity : 0.007 0.092 1601 Dihedral : 11.239 85.250 3511 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 0.10 % Allowed : 1.66 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.93 (0.16), residues: 1182 helix: -4.55 (0.08), residues: 679 sheet: -0.99 (0.68), residues: 55 loop : -2.94 (0.25), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 777 TYR 0.024 0.002 TYR B 253 PHE 0.023 0.003 PHE B 72 TRP 0.037 0.004 TRP B 946 HIS 0.010 0.002 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00684 ( 9391) covalent geometry : angle 1.05181 (12732) hydrogen bonds : bond 0.32975 ( 309) hydrogen bonds : angle 10.87516 ( 882) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 225 GLN cc_start: 0.8188 (tt0) cc_final: 0.7892 (tm-30) REVERT: B 477 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7691 (tt0) REVERT: B 565 LEU cc_start: 0.9298 (tp) cc_final: 0.8290 (tp) REVERT: B 883 GLN cc_start: 0.8236 (tp40) cc_final: 0.7783 (tp40) REVERT: B 985 ASP cc_start: 0.7924 (t70) cc_final: 0.7595 (t0) REVERT: B 998 GLU cc_start: 0.8213 (tt0) cc_final: 0.7958 (tm-30) REVERT: B 1138 LEU cc_start: 0.9048 (mt) cc_final: 0.8727 (mp) REVERT: B 1159 ARG cc_start: 0.6751 (mtt180) cc_final: 0.6239 (tpt90) outliers start: 1 outliers final: 0 residues processed: 231 average time/residue: 0.0899 time to fit residues: 27.4735 Evaluate side-chains 131 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.0170 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN B 303 ASN ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 954 HIS B1124 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.173528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.125095 restraints weight = 15828.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.129193 restraints weight = 7732.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.131882 restraints weight = 4874.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.133440 restraints weight = 3657.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.134533 restraints weight = 3081.531| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9392 Z= 0.178 Angle : 0.697 9.445 12732 Z= 0.372 Chirality : 0.044 0.219 1472 Planarity : 0.006 0.076 1601 Dihedral : 9.677 86.790 1429 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.80 % Allowed : 9.03 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.94 (0.18), residues: 1182 helix: -3.43 (0.13), residues: 725 sheet: -0.70 (0.70), residues: 55 loop : -2.96 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 353 TYR 0.018 0.002 TYR B1256 PHE 0.033 0.002 PHE B 72 TRP 0.020 0.002 TRP B 697 HIS 0.010 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 9391) covalent geometry : angle 0.69695 (12732) hydrogen bonds : bond 0.05512 ( 309) hydrogen bonds : angle 5.84301 ( 882) Misc. bond : bond 0.00072 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 515 ILE cc_start: 0.8758 (mt) cc_final: 0.8550 (tp) REVERT: B 805 ARG cc_start: 0.8400 (ttm110) cc_final: 0.7536 (ttm110) REVERT: B 809 ASP cc_start: 0.8376 (m-30) cc_final: 0.8115 (t0) REVERT: B 812 ASN cc_start: 0.8754 (m-40) cc_final: 0.8429 (m-40) REVERT: B 831 MET cc_start: 0.8156 (mmm) cc_final: 0.6660 (tmm) REVERT: B 883 GLN cc_start: 0.8135 (tp40) cc_final: 0.7681 (tp40) REVERT: B 1169 GLN cc_start: 0.8270 (tp40) cc_final: 0.7496 (tp-100) REVERT: B 1199 ARG cc_start: 0.8639 (mtm-85) cc_final: 0.8283 (mtm-85) REVERT: B 1202 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8668 (tp-100) outliers start: 27 outliers final: 15 residues processed: 180 average time/residue: 0.0699 time to fit residues: 17.3765 Evaluate side-chains 150 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 792 PHE Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1202 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 52 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 84 optimal weight: 0.1980 chunk 53 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN B 217 ASN B 883 GLN B1169 GLN B1250 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.174195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.125441 restraints weight = 15790.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.129687 restraints weight = 7671.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.132466 restraints weight = 4825.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.134054 restraints weight = 3612.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.135102 restraints weight = 3046.568| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9392 Z= 0.152 Angle : 0.626 8.804 12732 Z= 0.331 Chirality : 0.043 0.159 1472 Planarity : 0.004 0.064 1601 Dihedral : 9.145 88.382 1429 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.60 % Allowed : 9.97 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.86 (0.21), residues: 1182 helix: -2.45 (0.16), residues: 708 sheet: -0.57 (0.64), residues: 67 loop : -2.82 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 619 TYR 0.020 0.001 TYR B1256 PHE 0.025 0.002 PHE B 72 TRP 0.016 0.002 TRP B 765 HIS 0.009 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9391) covalent geometry : angle 0.62550 (12732) hydrogen bonds : bond 0.04175 ( 309) hydrogen bonds : angle 5.12463 ( 882) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7495 (p0) REVERT: B 440 ARG cc_start: 0.8154 (tpp80) cc_final: 0.7885 (tpp80) REVERT: B 615 MET cc_start: 0.5091 (mmp) cc_final: 0.4683 (mmt) REVERT: B 805 ARG cc_start: 0.8306 (ttm110) cc_final: 0.7593 (ttm110) REVERT: B 812 ASN cc_start: 0.8749 (m-40) cc_final: 0.8397 (m-40) REVERT: B 831 MET cc_start: 0.8182 (mmm) cc_final: 0.6821 (tmm) REVERT: B 883 GLN cc_start: 0.8114 (tp-100) cc_final: 0.7755 (tp40) REVERT: B 1055 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7099 (tt) REVERT: B 1134 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8270 (tm-30) REVERT: B 1138 LEU cc_start: 0.8867 (mp) cc_final: 0.8535 (mp) REVERT: B 1159 ARG cc_start: 0.8919 (tpt90) cc_final: 0.8685 (tpt90) REVERT: B 1202 GLN cc_start: 0.8971 (tp-100) cc_final: 0.8562 (tp-100) outliers start: 25 outliers final: 18 residues processed: 168 average time/residue: 0.0723 time to fit residues: 17.1856 Evaluate side-chains 154 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 792 PHE Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1134 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 11 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 ASN B 299 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.175639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.127310 restraints weight = 15709.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.131655 restraints weight = 7528.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134475 restraints weight = 4707.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.136104 restraints weight = 3515.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.137140 restraints weight = 2947.698| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9392 Z= 0.115 Angle : 0.582 8.684 12732 Z= 0.306 Chirality : 0.041 0.153 1472 Planarity : 0.004 0.060 1601 Dihedral : 8.768 85.063 1429 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.53 % Allowed : 10.38 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.22 (0.22), residues: 1182 helix: -1.89 (0.18), residues: 708 sheet: -0.23 (0.65), residues: 67 loop : -2.68 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1199 TYR 0.018 0.001 TYR B1256 PHE 0.028 0.001 PHE B 986 TRP 0.013 0.001 TRP B 101 HIS 0.007 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9391) covalent geometry : angle 0.58167 (12732) hydrogen bonds : bond 0.03337 ( 309) hydrogen bonds : angle 4.64551 ( 882) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ASP cc_start: 0.7875 (m-30) cc_final: 0.7630 (m-30) REVERT: B 346 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7471 (p0) REVERT: B 416 ILE cc_start: 0.9074 (mm) cc_final: 0.8870 (mm) REVERT: B 465 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8376 (mm) REVERT: B 615 MET cc_start: 0.5439 (mmp) cc_final: 0.5189 (mmt) REVERT: B 770 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: B 772 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8073 (tp) REVERT: B 805 ARG cc_start: 0.8413 (ttm110) cc_final: 0.7736 (ttm110) REVERT: B 809 ASP cc_start: 0.8394 (m-30) cc_final: 0.8144 (t0) REVERT: B 812 ASN cc_start: 0.8730 (m-40) cc_final: 0.8360 (m-40) REVERT: B 831 MET cc_start: 0.8277 (mmm) cc_final: 0.6913 (tmm) REVERT: B 883 GLN cc_start: 0.8027 (tp-100) cc_final: 0.7700 (tp40) REVERT: B 1043 ARG cc_start: 0.7908 (ptp-170) cc_final: 0.7629 (ptp-170) REVERT: B 1055 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6861 (tt) REVERT: B 1133 ILE cc_start: 0.9118 (pt) cc_final: 0.8733 (mm) REVERT: B 1134 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8139 (tm-30) REVERT: B 1138 LEU cc_start: 0.8777 (mp) cc_final: 0.8247 (mp) REVERT: B 1159 ARG cc_start: 0.8943 (tpt90) cc_final: 0.8699 (tpt90) REVERT: B 1202 GLN cc_start: 0.8888 (tp-100) cc_final: 0.8667 (tp-100) outliers start: 34 outliers final: 21 residues processed: 168 average time/residue: 0.0691 time to fit residues: 16.4888 Evaluate side-chains 155 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 792 PHE Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1134 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 65 optimal weight: 0.0770 chunk 68 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 89 optimal weight: 0.1980 chunk 69 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 0.1980 chunk 97 optimal weight: 9.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.179892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.133264 restraints weight = 15116.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.137708 restraints weight = 6995.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.140539 restraints weight = 4279.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.142201 restraints weight = 3136.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.142978 restraints weight = 2621.799| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9392 Z= 0.099 Angle : 0.573 9.862 12732 Z= 0.294 Chirality : 0.040 0.150 1472 Planarity : 0.004 0.057 1601 Dihedral : 8.427 88.073 1429 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.70 % Allowed : 13.40 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.87 (0.23), residues: 1182 helix: -1.50 (0.18), residues: 726 sheet: -0.28 (0.74), residues: 58 loop : -2.70 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 820 TYR 0.025 0.001 TYR B1256 PHE 0.031 0.001 PHE B 986 TRP 0.012 0.001 TRP B 101 HIS 0.007 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 9391) covalent geometry : angle 0.57280 (12732) hydrogen bonds : bond 0.02906 ( 309) hydrogen bonds : angle 4.33320 ( 882) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ASP cc_start: 0.7837 (m-30) cc_final: 0.7413 (m-30) REVERT: B 154 ASP cc_start: 0.7692 (m-30) cc_final: 0.7356 (t70) REVERT: B 321 LEU cc_start: 0.9281 (tp) cc_final: 0.9026 (tt) REVERT: B 346 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7370 (p0) REVERT: B 416 ILE cc_start: 0.9073 (mm) cc_final: 0.8858 (mm) REVERT: B 465 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8347 (mm) REVERT: B 615 MET cc_start: 0.6059 (mmp) cc_final: 0.5837 (mmt) REVERT: B 770 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6838 (mp0) REVERT: B 805 ARG cc_start: 0.8280 (ttm110) cc_final: 0.7643 (ttm110) REVERT: B 809 ASP cc_start: 0.8462 (m-30) cc_final: 0.8246 (t0) REVERT: B 812 ASN cc_start: 0.8645 (m-40) cc_final: 0.8258 (m-40) REVERT: B 831 MET cc_start: 0.8285 (mmm) cc_final: 0.6935 (tmm) REVERT: B 883 GLN cc_start: 0.7909 (tp-100) cc_final: 0.7671 (tp40) REVERT: B 968 VAL cc_start: 0.9114 (t) cc_final: 0.8892 (p) REVERT: B 1055 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6416 (mm) REVERT: B 1133 ILE cc_start: 0.9098 (pt) cc_final: 0.8732 (mm) REVERT: B 1134 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: B 1138 LEU cc_start: 0.8738 (mp) cc_final: 0.8210 (mp) REVERT: B 1159 ARG cc_start: 0.8899 (tpt90) cc_final: 0.8498 (tpt90) REVERT: B 1202 GLN cc_start: 0.8821 (tp-100) cc_final: 0.8525 (tp-100) outliers start: 26 outliers final: 14 residues processed: 163 average time/residue: 0.0835 time to fit residues: 18.9454 Evaluate side-chains 156 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 792 PHE Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1134 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 14 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 chunk 44 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.176935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.131555 restraints weight = 15596.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.135806 restraints weight = 7205.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.138534 restraints weight = 4384.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.140158 restraints weight = 3221.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.140901 restraints weight = 2694.127| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9392 Z= 0.103 Angle : 0.568 9.496 12732 Z= 0.292 Chirality : 0.041 0.149 1472 Planarity : 0.003 0.055 1601 Dihedral : 8.392 89.198 1429 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.12 % Allowed : 13.71 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.23), residues: 1182 helix: -1.22 (0.19), residues: 729 sheet: -0.16 (0.75), residues: 58 loop : -2.58 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 440 TYR 0.018 0.001 TYR B1256 PHE 0.034 0.001 PHE B 986 TRP 0.010 0.001 TRP B 101 HIS 0.008 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 9391) covalent geometry : angle 0.56835 (12732) hydrogen bonds : bond 0.02870 ( 309) hydrogen bonds : angle 4.19067 ( 882) Misc. bond : bond 0.00048 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ASP cc_start: 0.7846 (m-30) cc_final: 0.7429 (m-30) REVERT: B 154 ASP cc_start: 0.7809 (m-30) cc_final: 0.7476 (t70) REVERT: B 346 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7413 (p0) REVERT: B 416 ILE cc_start: 0.9138 (mm) cc_final: 0.8908 (mm) REVERT: B 465 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8347 (mm) REVERT: B 770 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: B 772 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8094 (tp) REVERT: B 805 ARG cc_start: 0.8353 (ttm110) cc_final: 0.7702 (ttm110) REVERT: B 809 ASP cc_start: 0.8414 (m-30) cc_final: 0.8166 (t0) REVERT: B 831 MET cc_start: 0.8346 (mmm) cc_final: 0.6880 (tmm) REVERT: B 883 GLN cc_start: 0.7955 (tp-100) cc_final: 0.7676 (tp40) REVERT: B 1055 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6329 (mm) REVERT: B 1133 ILE cc_start: 0.9118 (pt) cc_final: 0.8758 (mm) REVERT: B 1134 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8132 (tm-30) REVERT: B 1138 LEU cc_start: 0.8756 (mp) cc_final: 0.8285 (mp) REVERT: B 1202 GLN cc_start: 0.8950 (tp-100) cc_final: 0.8732 (tp-100) outliers start: 30 outliers final: 15 residues processed: 163 average time/residue: 0.0826 time to fit residues: 18.9941 Evaluate side-chains 158 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 792 PHE Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1134 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 17 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 23 optimal weight: 0.3980 chunk 94 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 75 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.178741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.133496 restraints weight = 15468.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.137735 restraints weight = 7168.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.140471 restraints weight = 4390.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.142018 restraints weight = 3236.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.143034 restraints weight = 2699.365| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9392 Z= 0.109 Angle : 0.595 9.682 12732 Z= 0.301 Chirality : 0.041 0.147 1472 Planarity : 0.003 0.056 1601 Dihedral : 8.140 86.263 1429 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.91 % Allowed : 14.64 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.24), residues: 1182 helix: -0.99 (0.19), residues: 729 sheet: -0.23 (0.77), residues: 59 loop : -2.48 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 440 TYR 0.018 0.001 TYR B1256 PHE 0.017 0.001 PHE B 33 TRP 0.033 0.001 TRP B 697 HIS 0.007 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9391) covalent geometry : angle 0.59500 (12732) hydrogen bonds : bond 0.02808 ( 309) hydrogen bonds : angle 4.12524 ( 882) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ASP cc_start: 0.7941 (m-30) cc_final: 0.7525 (m-30) REVERT: B 154 ASP cc_start: 0.7862 (m-30) cc_final: 0.7513 (t70) REVERT: B 346 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.7404 (p0) REVERT: B 416 ILE cc_start: 0.9130 (mm) cc_final: 0.8905 (mm) REVERT: B 465 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8394 (mm) REVERT: B 770 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: B 805 ARG cc_start: 0.8346 (ttm110) cc_final: 0.7697 (ttm110) REVERT: B 809 ASP cc_start: 0.8420 (m-30) cc_final: 0.8198 (t0) REVERT: B 831 MET cc_start: 0.8370 (mmm) cc_final: 0.6904 (tmm) REVERT: B 883 GLN cc_start: 0.7921 (tp-100) cc_final: 0.7649 (tp40) REVERT: B 968 VAL cc_start: 0.9096 (t) cc_final: 0.8869 (p) REVERT: B 1055 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6481 (mm) REVERT: B 1133 ILE cc_start: 0.9105 (pt) cc_final: 0.8754 (mm) REVERT: B 1134 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8312 (tm-30) outliers start: 28 outliers final: 16 residues processed: 157 average time/residue: 0.0773 time to fit residues: 17.2930 Evaluate side-chains 150 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 792 PHE Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1134 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 111 optimal weight: 0.0770 chunk 51 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.0870 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 ASN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.163743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.119991 restraints weight = 14830.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.121229 restraints weight = 9024.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.121895 restraints weight = 5920.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.122817 restraints weight = 5240.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.122855 restraints weight = 4930.510| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9392 Z= 0.103 Angle : 0.587 9.740 12732 Z= 0.295 Chirality : 0.041 0.146 1472 Planarity : 0.003 0.051 1601 Dihedral : 7.874 81.387 1429 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.49 % Allowed : 15.58 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.24), residues: 1182 helix: -0.83 (0.20), residues: 728 sheet: -0.26 (0.76), residues: 59 loop : -2.40 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1043 TYR 0.017 0.001 TYR B1256 PHE 0.017 0.001 PHE B 496 TRP 0.026 0.001 TRP B 697 HIS 0.007 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 9391) covalent geometry : angle 0.58680 (12732) hydrogen bonds : bond 0.02852 ( 309) hydrogen bonds : angle 4.13395 ( 882) Misc. bond : bond 0.00058 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ASP cc_start: 0.7905 (m-30) cc_final: 0.7530 (m-30) REVERT: B 154 ASP cc_start: 0.7795 (m-30) cc_final: 0.7373 (t70) REVERT: B 346 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7285 (p0) REVERT: B 416 ILE cc_start: 0.9060 (mm) cc_final: 0.8815 (mm) REVERT: B 465 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8391 (mm) REVERT: B 770 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: B 805 ARG cc_start: 0.8252 (ttm110) cc_final: 0.7597 (ttm110) REVERT: B 831 MET cc_start: 0.8285 (mmm) cc_final: 0.7017 (tmm) REVERT: B 943 LEU cc_start: 0.7645 (tt) cc_final: 0.7066 (mm) REVERT: B 968 VAL cc_start: 0.9145 (t) cc_final: 0.8905 (p) REVERT: B 1133 ILE cc_start: 0.9115 (pt) cc_final: 0.8808 (mm) REVERT: B 1134 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8332 (tm-30) outliers start: 24 outliers final: 16 residues processed: 150 average time/residue: 0.0897 time to fit residues: 19.1541 Evaluate side-chains 147 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 792 PHE Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1134 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 18 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.0370 chunk 19 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 12 optimal weight: 0.0570 chunk 63 optimal weight: 1.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.164032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117803 restraints weight = 14814.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.121245 restraints weight = 8010.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123513 restraints weight = 5341.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.124936 restraints weight = 4108.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.125646 restraints weight = 3494.208| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9392 Z= 0.102 Angle : 0.586 9.727 12732 Z= 0.296 Chirality : 0.041 0.145 1472 Planarity : 0.003 0.051 1601 Dihedral : 7.680 81.075 1429 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.39 % Allowed : 15.99 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.24), residues: 1182 helix: -0.73 (0.20), residues: 729 sheet: -0.16 (0.74), residues: 61 loop : -2.30 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 893 TYR 0.016 0.001 TYR B1256 PHE 0.016 0.001 PHE B 33 TRP 0.024 0.001 TRP B 697 HIS 0.006 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 9391) covalent geometry : angle 0.58594 (12732) hydrogen bonds : bond 0.02844 ( 309) hydrogen bonds : angle 4.09971 ( 882) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ASP cc_start: 0.7855 (m-30) cc_final: 0.7517 (m-30) REVERT: B 154 ASP cc_start: 0.7676 (m-30) cc_final: 0.7411 (t70) REVERT: B 346 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.7242 (p0) REVERT: B 416 ILE cc_start: 0.9089 (mm) cc_final: 0.8868 (mm) REVERT: B 465 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8469 (mm) REVERT: B 770 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6780 (mp0) REVERT: B 805 ARG cc_start: 0.8271 (ttm110) cc_final: 0.7682 (ttm110) REVERT: B 831 MET cc_start: 0.8223 (mmm) cc_final: 0.6927 (tmm) REVERT: B 943 LEU cc_start: 0.7610 (tt) cc_final: 0.7095 (mm) REVERT: B 968 VAL cc_start: 0.9116 (t) cc_final: 0.8903 (p) REVERT: B 1055 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6349 (mm) REVERT: B 1133 ILE cc_start: 0.9067 (pt) cc_final: 0.8751 (mm) REVERT: B 1134 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: B 1138 LEU cc_start: 0.8713 (mp) cc_final: 0.8325 (mp) outliers start: 23 outliers final: 16 residues processed: 143 average time/residue: 0.0820 time to fit residues: 16.9871 Evaluate side-chains 148 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 792 PHE Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1134 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 114 optimal weight: 0.0040 chunk 51 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 0.0070 chunk 5 optimal weight: 0.0770 chunk 81 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 overall best weight: 0.3568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.165572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.119735 restraints weight = 14761.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123301 restraints weight = 7994.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.125584 restraints weight = 5273.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.127019 restraints weight = 4033.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.127735 restraints weight = 3422.366| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9392 Z= 0.096 Angle : 0.581 9.803 12732 Z= 0.292 Chirality : 0.040 0.142 1472 Planarity : 0.003 0.049 1601 Dihedral : 7.419 79.768 1429 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.28 % Allowed : 15.89 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.25), residues: 1182 helix: -0.54 (0.20), residues: 724 sheet: 0.14 (0.75), residues: 59 loop : -2.21 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 893 TYR 0.016 0.001 TYR B1256 PHE 0.016 0.001 PHE B 33 TRP 0.023 0.001 TRP B 697 HIS 0.006 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 9391) covalent geometry : angle 0.58068 (12732) hydrogen bonds : bond 0.02664 ( 309) hydrogen bonds : angle 4.03331 ( 882) Misc. bond : bond 0.00063 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ASP cc_start: 0.7796 (m-30) cc_final: 0.7464 (m-30) REVERT: B 154 ASP cc_start: 0.7723 (m-30) cc_final: 0.7290 (t70) REVERT: B 157 MET cc_start: 0.8514 (tmm) cc_final: 0.8278 (ppp) REVERT: B 346 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7203 (p0) REVERT: B 389 PHE cc_start: 0.8095 (t80) cc_final: 0.7717 (t80) REVERT: B 416 ILE cc_start: 0.9065 (mm) cc_final: 0.8837 (mm) REVERT: B 465 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8400 (mm) REVERT: B 735 TYR cc_start: 0.7958 (t80) cc_final: 0.7717 (t80) REVERT: B 770 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: B 831 MET cc_start: 0.8217 (mmm) cc_final: 0.6922 (tmm) REVERT: B 943 LEU cc_start: 0.7533 (tt) cc_final: 0.7045 (mm) REVERT: B 1055 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6251 (mm) REVERT: B 1133 ILE cc_start: 0.9055 (pt) cc_final: 0.8745 (mm) REVERT: B 1134 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8196 (tm-30) REVERT: B 1138 LEU cc_start: 0.8728 (mp) cc_final: 0.8314 (mp) outliers start: 22 outliers final: 15 residues processed: 153 average time/residue: 0.0835 time to fit residues: 18.5324 Evaluate side-chains 148 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 792 PHE Chi-restraints excluded: chain B residue 883 GLN Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1134 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 105 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 78 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.164603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.121049 restraints weight = 14724.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.122306 restraints weight = 8661.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.123134 restraints weight = 5407.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123808 restraints weight = 5491.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123868 restraints weight = 4610.522| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 9392 Z= 0.193 Angle : 0.880 59.200 12732 Z= 0.498 Chirality : 0.045 0.700 1472 Planarity : 0.003 0.050 1601 Dihedral : 7.431 79.776 1429 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.28 % Allowed : 16.20 % Favored : 81.52 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.25), residues: 1182 helix: -0.56 (0.20), residues: 724 sheet: 0.14 (0.75), residues: 59 loop : -2.21 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.000 ARG B 688 TYR 0.015 0.001 TYR B1256 PHE 0.041 0.001 PHE B 997 TRP 0.021 0.001 TRP B 697 HIS 0.006 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 9391) covalent geometry : angle 0.88029 (12732) hydrogen bonds : bond 0.02655 ( 309) hydrogen bonds : angle 4.03457 ( 882) Misc. bond : bond 0.00062 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1446.71 seconds wall clock time: 25 minutes 36.50 seconds (1536.50 seconds total)