Starting phenix.real_space_refine on Wed Apr 30 07:46:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zq4_60370/04_2025/8zq4_60370.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zq4_60370/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zq4_60370/04_2025/8zq4_60370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zq4_60370/04_2025/8zq4_60370.map" model { file = "/net/cci-nas-00/data/ceres_data/8zq4_60370/04_2025/8zq4_60370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zq4_60370/04_2025/8zq4_60370.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 6.08, per 1000 atoms: 0.66 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: 2.49 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.35 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: 3.16 Time building geometry restraints manager: 2.96 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: 1.200 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.820 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.720 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.037 0.004 TRP B 946 HIS 0.010 0.002 HIS B 347 PHE 0.023 0.003 PHE B 72 TYR 0.024 0.002 TYR B 253 ARG 0.007 0.001 ARG B 777 Details of bonding type rmsd hydrogen bonds : bond 0.32975 ( 309) hydrogen bonds : angle 10.87516 ( 882) covalent geometry : bond 0.00684 ( 9391) covalent geometry : angle 1.05181 (12732) 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 : 1.056 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: 0.7891 (tm-30) REVERT: B 319 LEU cc_start: 0.8925 (mt) cc_final: 0.8571 (mt) 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: 0.8291 (tp) REVERT: B 883 GLN cc_start: 0.8236 (tp40) cc_final: 0.7787 (tp40) REVERT: B 985 ASP cc_start: 0.7924 (t70) cc_final: 0.7597 (t0) REVERT: B 998 GLU cc_start: 0.8213 (tt0) cc_final: 0.7958 (tm-30) REVERT: B 1048 ARG cc_start: 0.7624 (ttt180) cc_final: 0.7201 (ptm-80) 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: 0.2658 time to fit residues: 81.1384 Evaluate side-chains 132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.0070 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 overall best weight: 2.1204 ------------------------------------------------------------------------------- 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 607 GLN B 883 GLN B 954 HIS B1124 HIS B1169 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.170732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.121235 restraints weight = 15865.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.125218 restraints weight = 7963.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.127828 restraints weight = 5114.633| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9392 Z= 0.240 Angle : 0.752 9.199 12732 Z= 0.400 Chirality : 0.046 0.221 1472 Planarity : 0.006 0.074 1601 Dihedral : 9.930 87.785 1429 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 3.01 % Allowed : 8.52 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.19), residues: 1182 helix: -3.40 (0.13), residues: 726 sheet: -1.00 (0.63), residues: 67 loop : -2.98 (0.27), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 697 HIS 0.010 0.001 HIS B 588 PHE 0.036 0.002 PHE B 72 TYR 0.019 0.002 TYR B1122 ARG 0.004 0.001 ARG B 353 Details of bonding type rmsd hydrogen bonds : bond 0.05281 ( 309) hydrogen bonds : angle 5.90713 ( 882) covalent geometry : bond 0.00542 ( 9391) covalent geometry : angle 0.75230 (12732) Misc. bond : bond 0.00090 ( 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 193 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.969 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 805 ARG cc_start: 0.8488 (ttm110) cc_final: 0.7720 (ttm110) REVERT: B 809 ASP cc_start: 0.8432 (m-30) cc_final: 0.8190 (t0) REVERT: B 812 ASN cc_start: 0.8824 (m-40) cc_final: 0.8495 (m-40) REVERT: B 831 MET cc_start: 0.8132 (mmm) cc_final: 0.6678 (tmm) REVERT: B 883 GLN cc_start: 0.8159 (tp-100) cc_final: 0.7740 (tp40) REVERT: B 985 ASP cc_start: 0.7645 (t70) cc_final: 0.7308 (t0) REVERT: B 998 GLU cc_start: 0.8283 (tt0) cc_final: 0.7943 (tm-30) REVERT: B 1055 LEU cc_start: 0.7685 (tt) cc_final: 0.7398 (tt) REVERT: B 1169 GLN cc_start: 0.8184 (tp-100) cc_final: 0.7453 (tp-100) REVERT: B 1199 ARG cc_start: 0.8822 (mtm-85) cc_final: 0.8602 (mtm-85) REVERT: B 1202 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8793 (tp-100) outliers start: 29 outliers final: 15 residues processed: 184 average time/residue: 0.2372 time to fit residues: 59.1979 Evaluate side-chains 155 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 LEU 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 1104 ILE 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 57 optimal weight: 20.0000 chunk 86 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 0.0970 chunk 44 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 11 optimal weight: 0.0980 chunk 85 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 299 HIS B1250 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.175613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.127887 restraints weight = 15830.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.132269 restraints weight = 7478.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.135099 restraints weight = 4629.612| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9392 Z= 0.109 Angle : 0.605 8.821 12732 Z= 0.321 Chirality : 0.041 0.169 1472 Planarity : 0.004 0.064 1601 Dihedral : 9.048 89.943 1429 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.39 % Allowed : 10.59 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.21), residues: 1182 helix: -2.41 (0.16), residues: 711 sheet: -0.54 (0.64), residues: 67 loop : -2.84 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 697 HIS 0.009 0.001 HIS B 588 PHE 0.022 0.001 PHE B 72 TYR 0.018 0.001 TYR B1256 ARG 0.006 0.001 ARG B1048 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 309) hydrogen bonds : angle 5.01244 ( 882) covalent geometry : bond 0.00227 ( 9391) covalent geometry : angle 0.60489 (12732) Misc. bond : bond 0.00018 ( 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 190 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 1.101 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: 0.7871 (m-30) cc_final: 0.7394 (m-30) REVERT: B 315 MET cc_start: 0.7887 (mmm) cc_final: 0.7009 (mtp) REVERT: B 346 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7536 (p0) REVERT: B 615 MET cc_start: 0.4983 (mmp) cc_final: 0.4626 (mmt) REVERT: B 805 ARG cc_start: 0.8443 (ttm110) cc_final: 0.7630 (ttm110) REVERT: B 812 ASN cc_start: 0.8785 (m-40) cc_final: 0.8412 (m-40) REVERT: B 831 MET cc_start: 0.8108 (mmm) cc_final: 0.6755 (tmm) REVERT: B 883 GLN cc_start: 0.8082 (tp-100) cc_final: 0.7787 (tp40) REVERT: B 1042 PHE cc_start: 0.7781 (m-80) cc_final: 0.7508 (m-80) REVERT: B 1055 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7023 (tt) REVERT: B 1104 ILE cc_start: 0.8705 (tt) cc_final: 0.8288 (pt) REVERT: B 1134 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8349 (tm-30) REVERT: B 1138 LEU cc_start: 0.8871 (mp) cc_final: 0.8123 (mp) REVERT: B 1203 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8096 (tm-30) outliers start: 23 outliers final: 12 residues processed: 181 average time/residue: 0.2232 time to fit residues: 56.1138 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 : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 TRP 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 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 558 THR Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 792 PHE Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1134 GLN Chi-restraints excluded: chain B residue 1203 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 100 optimal weight: 5.9990 chunk 77 optimal weight: 0.2980 chunk 5 optimal weight: 4.9990 chunk 18 optimal weight: 0.0980 chunk 44 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 110 optimal weight: 0.0570 chunk 105 optimal weight: 0.5980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 347 HIS ** 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 = 0.4295 r_free = 0.4295 target = 0.178843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.134046 restraints weight = 14844.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.138177 restraints weight = 6922.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.140814 restraints weight = 4208.781| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9392 Z= 0.101 Angle : 0.580 8.653 12732 Z= 0.302 Chirality : 0.041 0.149 1472 Planarity : 0.004 0.058 1601 Dihedral : 8.680 86.307 1429 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.70 % Allowed : 12.15 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.22), residues: 1182 helix: -1.88 (0.18), residues: 726 sheet: -0.30 (0.66), residues: 68 loop : -2.93 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 765 HIS 0.006 0.001 HIS B 588 PHE 0.029 0.001 PHE B 986 TYR 0.019 0.001 TYR B1256 ARG 0.005 0.000 ARG B 569 Details of bonding type rmsd hydrogen bonds : bond 0.03095 ( 309) hydrogen bonds : angle 4.57204 ( 882) covalent geometry : bond 0.00210 ( 9391) covalent geometry : angle 0.58007 (12732) Misc. bond : bond 0.00038 ( 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 180 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 1.084 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: 0.7793 (m-30) cc_final: 0.7316 (m-30) REVERT: B 315 MET cc_start: 0.7762 (mmm) cc_final: 0.6946 (mtp) REVERT: B 346 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7476 (p0) REVERT: B 416 ILE cc_start: 0.9055 (mm) cc_final: 0.8834 (mm) REVERT: B 421 ASP cc_start: 0.8096 (t0) cc_final: 0.7862 (t0) REVERT: B 688 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8234 (ttt90) REVERT: B 770 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6734 (mp0) REVERT: B 805 ARG cc_start: 0.8318 (ttm110) cc_final: 0.7618 (ttm110) REVERT: B 809 ASP cc_start: 0.8380 (m-30) cc_final: 0.8115 (t0) REVERT: B 812 ASN cc_start: 0.8710 (m-40) cc_final: 0.8325 (m-40) REVERT: B 831 MET cc_start: 0.8042 (mmm) cc_final: 0.6782 (tmm) REVERT: B 883 GLN cc_start: 0.7925 (tp-100) cc_final: 0.7686 (tp40) REVERT: B 1055 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6825 (tt) REVERT: B 1133 ILE cc_start: 0.9111 (pt) cc_final: 0.8720 (mm) REVERT: B 1134 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8114 (tm-30) REVERT: B 1138 LEU cc_start: 0.8755 (mp) cc_final: 0.8213 (mp) REVERT: B 1199 ARG cc_start: 0.8830 (mtm-85) cc_final: 0.8271 (mtm-85) REVERT: B 1203 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8051 (tm-30) REVERT: B 1234 ASP cc_start: 0.8146 (p0) cc_final: 0.7892 (t0) outliers start: 26 outliers final: 13 residues processed: 171 average time/residue: 0.2081 time to fit residues: 50.0178 Evaluate side-chains 152 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 203 VAL 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 448 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 688 ARG 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 1134 GLN Chi-restraints excluded: chain B residue 1203 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 91 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 94 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 61 optimal weight: 0.0870 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 0.0770 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 HIS B 217 ASN ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.181492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.135414 restraints weight = 15134.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.139746 restraints weight = 7092.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.142559 restraints weight = 4369.587| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9392 Z= 0.096 Angle : 0.564 9.070 12732 Z= 0.289 Chirality : 0.040 0.146 1472 Planarity : 0.004 0.057 1601 Dihedral : 8.543 88.711 1429 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.01 % Allowed : 13.40 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.23), residues: 1182 helix: -1.45 (0.18), residues: 725 sheet: -0.45 (0.74), residues: 59 loop : -2.67 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 765 HIS 0.007 0.001 HIS B 588 PHE 0.031 0.001 PHE B 986 TYR 0.024 0.001 TYR B1256 ARG 0.004 0.000 ARG B1048 Details of bonding type rmsd hydrogen bonds : bond 0.02878 ( 309) hydrogen bonds : angle 4.32183 ( 882) covalent geometry : bond 0.00207 ( 9391) covalent geometry : angle 0.56364 (12732) Misc. bond : bond 0.00050 ( 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 175 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 1.115 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: 0.7401 (m-30) REVERT: B 154 ASP cc_start: 0.7791 (m-30) cc_final: 0.7392 (t70) REVERT: B 346 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7514 (p0) REVERT: B 416 ILE cc_start: 0.9086 (mm) cc_final: 0.8873 (mm) REVERT: B 421 ASP cc_start: 0.8085 (t0) cc_final: 0.7742 (t0) REVERT: B 465 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8383 (mm) REVERT: B 558 THR cc_start: 0.9015 (m) cc_final: 0.8531 (p) REVERT: B 578 GLN cc_start: 0.8826 (tt0) cc_final: 0.8538 (pt0) REVERT: B 688 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8230 (ttt180) REVERT: B 770 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6754 (mp0) REVERT: B 809 ASP cc_start: 0.8482 (m-30) cc_final: 0.8224 (t0) REVERT: B 831 MET cc_start: 0.8216 (mmm) cc_final: 0.6800 (tmm) REVERT: B 883 GLN cc_start: 0.7907 (tp-100) cc_final: 0.7677 (tp40) REVERT: B 1055 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6405 (mm) REVERT: B 1133 ILE cc_start: 0.9144 (pt) cc_final: 0.8780 (mm) REVERT: B 1134 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8154 (tm-30) REVERT: B 1138 LEU cc_start: 0.8766 (mp) cc_final: 0.8276 (mp) outliers start: 29 outliers final: 12 residues processed: 164 average time/residue: 0.2127 time to fit residues: 48.7907 Evaluate side-chains 152 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 346 ASP 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 599 VAL Chi-restraints excluded: chain B residue 688 ARG 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 1058 VAL 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 12 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 20.0000 chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 607 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.178100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.132831 restraints weight = 15290.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.137018 restraints weight = 7182.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.139694 restraints weight = 4409.120| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9392 Z= 0.116 Angle : 0.582 8.369 12732 Z= 0.298 Chirality : 0.041 0.152 1472 Planarity : 0.004 0.056 1601 Dihedral : 8.344 86.755 1429 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.49 % Allowed : 14.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.24), residues: 1182 helix: -1.21 (0.19), residues: 731 sheet: -0.32 (0.75), residues: 59 loop : -2.55 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 765 HIS 0.008 0.001 HIS B 588 PHE 0.034 0.001 PHE B 986 TYR 0.023 0.001 TYR B1256 ARG 0.003 0.000 ARG B 569 Details of bonding type rmsd hydrogen bonds : bond 0.03059 ( 309) hydrogen bonds : angle 4.27479 ( 882) covalent geometry : bond 0.00258 ( 9391) covalent geometry : angle 0.58186 (12732) Misc. bond : bond 0.00046 ( 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 166 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.991 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: 0.7955 (m-30) cc_final: 0.7529 (m-30) REVERT: B 154 ASP cc_start: 0.7897 (m-30) cc_final: 0.7497 (t70) REVERT: B 346 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7411 (p0) REVERT: B 416 ILE cc_start: 0.9105 (mm) cc_final: 0.8872 (mm) REVERT: B 421 ASP cc_start: 0.8094 (t0) cc_final: 0.7718 (t0) REVERT: B 465 LEU cc_start: 0.8664 (mm) cc_final: 0.8402 (mm) REVERT: B 578 GLN cc_start: 0.8754 (tt0) cc_final: 0.8495 (pt0) REVERT: B 688 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8065 (ttt90) REVERT: B 770 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: B 809 ASP cc_start: 0.8527 (m-30) cc_final: 0.8227 (t0) REVERT: B 831 MET cc_start: 0.8246 (mmm) cc_final: 0.6860 (tmm) REVERT: B 883 GLN cc_start: 0.7909 (tp-100) cc_final: 0.7702 (tp40) REVERT: B 968 VAL cc_start: 0.9128 (t) cc_final: 0.8894 (p) REVERT: B 1133 ILE cc_start: 0.9120 (pt) cc_final: 0.8777 (mm) REVERT: B 1134 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: B 1138 LEU cc_start: 0.8753 (mp) cc_final: 0.8266 (mp) REVERT: B 1203 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8088 (tm-30) outliers start: 24 outliers final: 15 residues processed: 157 average time/residue: 0.2074 time to fit residues: 46.1998 Evaluate side-chains 153 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 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 413 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 688 ARG 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 1134 GLN Chi-restraints excluded: chain B residue 1203 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 86 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 0.0040 chunk 106 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.177852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.132854 restraints weight = 15469.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.136982 restraints weight = 7298.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.139627 restraints weight = 4481.942| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9392 Z= 0.118 Angle : 0.589 9.724 12732 Z= 0.299 Chirality : 0.042 0.197 1472 Planarity : 0.003 0.054 1601 Dihedral : 8.100 80.812 1429 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.60 % Allowed : 15.58 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.24), residues: 1182 helix: -0.98 (0.20), residues: 717 sheet: -0.30 (0.75), residues: 59 loop : -2.23 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 697 HIS 0.008 0.001 HIS B 588 PHE 0.016 0.001 PHE B 33 TYR 0.023 0.001 TYR B1256 ARG 0.003 0.000 ARG B1048 Details of bonding type rmsd hydrogen bonds : bond 0.02994 ( 309) hydrogen bonds : angle 4.23651 ( 882) covalent geometry : bond 0.00269 ( 9391) covalent geometry : angle 0.58922 (12732) Misc. bond : bond 0.00054 ( 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 159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.035 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: 0.7924 (m-30) cc_final: 0.7599 (m-30) REVERT: B 416 ILE cc_start: 0.9075 (mm) cc_final: 0.8835 (mm) REVERT: B 465 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8386 (mm) REVERT: B 578 GLN cc_start: 0.8721 (tt0) cc_final: 0.8481 (pt0) REVERT: B 688 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7963 (ttt90) REVERT: B 770 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: B 831 MET cc_start: 0.8285 (mmm) cc_final: 0.7006 (tmm) REVERT: B 1055 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6479 (mm) REVERT: B 1133 ILE cc_start: 0.9095 (pt) cc_final: 0.8757 (mm) REVERT: B 1134 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8260 (tm-30) REVERT: B 1203 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: B 1207 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8214 (pm20) outliers start: 25 outliers final: 14 residues processed: 150 average time/residue: 0.2039 time to fit residues: 43.9590 Evaluate side-chains 145 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL 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 203 VAL 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 599 VAL Chi-restraints excluded: chain B residue 688 ARG 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 1055 LEU Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1134 GLN Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain B residue 1207 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 16 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 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 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 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 = 0.4279 r_free = 0.4279 target = 0.177843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.132747 restraints weight = 15735.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.136949 restraints weight = 7382.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.139636 restraints weight = 4507.038| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4674 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= 0.114 Angle : 0.599 9.906 12732 Z= 0.302 Chirality : 0.042 0.212 1472 Planarity : 0.003 0.050 1601 Dihedral : 7.939 80.958 1429 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.49 % Allowed : 16.51 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.24), residues: 1182 helix: -0.90 (0.20), residues: 728 sheet: -0.29 (0.75), residues: 59 loop : -2.30 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 697 HIS 0.006 0.001 HIS B 588 PHE 0.016 0.001 PHE B 986 TYR 0.025 0.001 TYR B1256 ARG 0.003 0.000 ARG B1048 Details of bonding type rmsd hydrogen bonds : bond 0.03029 ( 309) hydrogen bonds : angle 4.21684 ( 882) covalent geometry : bond 0.00256 ( 9391) covalent geometry : angle 0.59939 (12732) Misc. bond : bond 0.00056 ( 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 158 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 1.029 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: 0.7966 (m-30) cc_final: 0.7569 (m-30) REVERT: B 416 ILE cc_start: 0.9131 (mm) cc_final: 0.8916 (mm) REVERT: B 437 LEU cc_start: 0.8651 (mm) cc_final: 0.8372 (mm) REVERT: B 465 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8373 (mm) REVERT: B 578 GLN cc_start: 0.8889 (tt0) cc_final: 0.8580 (pt0) REVERT: B 770 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: B 831 MET cc_start: 0.8344 (mmm) cc_final: 0.6919 (tmm) REVERT: B 1055 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6402 (mm) REVERT: B 1133 ILE cc_start: 0.9126 (pt) cc_final: 0.8820 (mm) REVERT: B 1134 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8360 (tm-30) REVERT: B 1203 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8113 (tm-30) REVERT: B 1207 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8219 (pm20) outliers start: 24 outliers final: 17 residues processed: 150 average time/residue: 0.1891 time to fit residues: 41.6549 Evaluate side-chains 149 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL 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 203 VAL 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 599 VAL Chi-restraints excluded: chain B residue 688 ARG 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 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 Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain B residue 1207 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 34 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 0.0060 chunk 65 optimal weight: 0.0670 chunk 106 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 overall best weight: 0.5134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN ** B 883 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 = 0.4063 r_free = 0.4063 target = 0.166737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.119623 restraints weight = 14521.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.122874 restraints weight = 8164.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.125003 restraints weight = 5580.046| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4854 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= 0.103 Angle : 0.598 10.302 12732 Z= 0.301 Chirality : 0.041 0.210 1472 Planarity : 0.003 0.052 1601 Dihedral : 7.693 79.849 1429 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.91 % Allowed : 16.41 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.24), residues: 1182 helix: -0.75 (0.20), residues: 728 sheet: -0.32 (0.74), residues: 59 loop : -2.26 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 697 HIS 0.005 0.001 HIS B 588 PHE 0.014 0.001 PHE B 986 TYR 0.025 0.001 TYR B1256 ARG 0.003 0.000 ARG B 805 Details of bonding type rmsd hydrogen bonds : bond 0.02842 ( 309) hydrogen bonds : angle 4.13486 ( 882) covalent geometry : bond 0.00226 ( 9391) covalent geometry : angle 0.59845 (12732) Misc. bond : bond 0.00064 ( 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 160 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.996 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: 0.7850 (m-30) cc_final: 0.7518 (m-30) REVERT: B 416 ILE cc_start: 0.9084 (mm) cc_final: 0.8869 (mm) REVERT: B 437 LEU cc_start: 0.8486 (mm) cc_final: 0.8204 (mm) REVERT: B 465 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8356 (mm) REVERT: B 578 GLN cc_start: 0.8789 (tt0) cc_final: 0.8517 (pt0) REVERT: B 770 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: B 831 MET cc_start: 0.8212 (mmm) cc_final: 0.7051 (tmm) REVERT: B 943 LEU cc_start: 0.7674 (tt) cc_final: 0.7162 (mm) REVERT: B 1055 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6334 (mm) REVERT: B 1133 ILE cc_start: 0.9086 (pt) cc_final: 0.8783 (mm) REVERT: B 1134 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: B 1184 MET cc_start: 0.7403 (tmm) cc_final: 0.6908 (tmm) REVERT: B 1203 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8111 (tm-30) REVERT: B 1207 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8191 (pm20) outliers start: 28 outliers final: 16 residues processed: 149 average time/residue: 0.1895 time to fit residues: 40.9400 Evaluate side-chains 147 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 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 688 ARG 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 1024 VAL Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1134 GLN Chi-restraints excluded: chain B residue 1159 ARG Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain B residue 1207 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 117 optimal weight: 0.0770 chunk 93 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 90 optimal weight: 0.0020 chunk 104 optimal weight: 6.9990 overall best weight: 0.5346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 883 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 = 0.4037 r_free = 0.4037 target = 0.164888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.121431 restraints weight = 14796.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.121268 restraints weight = 9673.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122423 restraints weight = 6507.868| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9392 Z= 0.105 Angle : 0.602 10.115 12732 Z= 0.302 Chirality : 0.041 0.216 1472 Planarity : 0.003 0.058 1601 Dihedral : 7.571 79.352 1429 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.28 % Allowed : 17.03 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.24), residues: 1182 helix: -0.69 (0.20), residues: 727 sheet: -0.05 (0.76), residues: 57 loop : -2.22 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 697 HIS 0.005 0.001 HIS B 588 PHE 0.014 0.001 PHE B 986 TYR 0.025 0.001 TYR B1256 ARG 0.002 0.000 ARG B1048 Details of bonding type rmsd hydrogen bonds : bond 0.02849 ( 309) hydrogen bonds : angle 4.09746 ( 882) covalent geometry : bond 0.00239 ( 9391) covalent geometry : angle 0.60187 (12732) Misc. bond : bond 0.00062 ( 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 155 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 1.055 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: 0.7877 (m-30) cc_final: 0.7534 (m-30) REVERT: B 416 ILE cc_start: 0.9074 (mm) cc_final: 0.8848 (mm) REVERT: B 437 LEU cc_start: 0.8651 (mm) cc_final: 0.8376 (mm) REVERT: B 465 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8352 (mm) REVERT: B 578 GLN cc_start: 0.8799 (tt0) cc_final: 0.8539 (pt0) REVERT: B 688 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7904 (ttp80) REVERT: B 770 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: B 831 MET cc_start: 0.8217 (mmm) cc_final: 0.6985 (tmm) REVERT: B 943 LEU cc_start: 0.7656 (tt) cc_final: 0.7142 (mm) REVERT: B 1055 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6293 (mm) REVERT: B 1133 ILE cc_start: 0.9123 (pt) cc_final: 0.8841 (mm) REVERT: B 1134 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8326 (tm-30) REVERT: B 1138 LEU cc_start: 0.8751 (mp) cc_final: 0.8369 (mp) outliers start: 22 outliers final: 13 residues processed: 147 average time/residue: 0.1959 time to fit residues: 41.6096 Evaluate side-chains 144 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 171 HIS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 212 LEU 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 688 ARG 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 1055 LEU Chi-restraints excluded: chain B residue 1134 GLN Chi-restraints excluded: chain B residue 1159 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 111 optimal weight: 6.9990 chunk 108 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 72 optimal weight: 0.2980 chunk 98 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 883 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 = 0.4018 r_free = 0.4018 target = 0.163587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.117624 restraints weight = 15725.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.118597 restraints weight = 9310.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.118436 restraints weight = 6417.559| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9392 Z= 0.115 Angle : 0.620 9.863 12732 Z= 0.312 Chirality : 0.041 0.205 1472 Planarity : 0.003 0.055 1601 Dihedral : 7.556 80.022 1429 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.97 % Allowed : 17.65 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.24), residues: 1182 helix: -0.60 (0.20), residues: 721 sheet: -0.13 (0.74), residues: 57 loop : -2.16 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 697 HIS 0.005 0.001 HIS B 588 PHE 0.015 0.001 PHE B 986 TYR 0.024 0.001 TYR B1256 ARG 0.002 0.000 ARG B1048 Details of bonding type rmsd hydrogen bonds : bond 0.02944 ( 309) hydrogen bonds : angle 4.14670 ( 882) covalent geometry : bond 0.00264 ( 9391) covalent geometry : angle 0.61958 (12732) Misc. bond : bond 0.00061 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3334.72 seconds wall clock time: 58 minutes 39.20 seconds (3519.20 seconds total)