Starting phenix.real_space_refine on Sat Aug 23 02:36:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpz_60369/08_2025/8zpz_60369.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpz_60369/08_2025/8zpz_60369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zpz_60369/08_2025/8zpz_60369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpz_60369/08_2025/8zpz_60369.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zpz_60369/08_2025/8zpz_60369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpz_60369/08_2025/8zpz_60369.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 5828 2.51 5 N 1556 2.21 5 O 1676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9103 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 9069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1179, 9069 Classifications: {'peptide': 1179} Link IDs: {'PTRANS': 30, 'TRANS': 1148} Chain breaks: 2 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'BLD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.38, per 1000 atoms: 0.26 Number of scatterers: 9103 At special positions: 0 Unit cell: (72.6, 106.7, 143, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1676 8.00 N 1556 7.00 C 5828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 362.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 6 sheets defined 61.2% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'B' and resid 37 through 42 removed outlier: 3.608A pdb=" N TYR B 41 " --> pdb=" O GLY B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 56 Processing helix chain 'B' and resid 57 through 74 removed outlier: 3.828A pdb=" N ARG B 63 " --> pdb=" O PRO B 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.567A pdb=" N LYS B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 97 through 109 removed outlier: 3.925A pdb=" N SER B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP B 105 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 107 " --> pdb=" O SER B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 removed outlier: 3.602A pdb=" N ARG B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 145 through 153 removed outlier: 3.858A pdb=" N PHE B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 151 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 161 removed outlier: 3.892A pdb=" N VAL B 158 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 161 " --> pdb=" O MET B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 185 removed outlier: 3.676A pdb=" N ILE B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE B 176 " --> pdb=" O TYR B 172 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 180 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 181 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 185 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 removed outlier: 4.512A pdb=" N VAL B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 217 removed outlier: 3.745A pdb=" N ILE B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY B 206 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR B 209 " --> pdb=" O GLY B 205 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 226 removed outlier: 3.552A pdb=" N ALA B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 236 removed outlier: 3.816A pdb=" N GLU B 231 " --> pdb=" O GLY B 227 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 236 " --> pdb=" O GLN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 258 through 273 removed outlier: 3.686A pdb=" N LEU B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B 266 " --> pdb=" O LYS B 262 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY B 268 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 269 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 270 " --> pdb=" O LYS B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 299 removed outlier: 3.749A pdb=" N TYR B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B 280 " --> pdb=" O GLY B 276 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS B 284 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TRP B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B 298 " --> pdb=" O GLY B 294 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS B 299 " --> pdb=" O TYR B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 319 Processing helix chain 'B' and resid 321 through 323 No H-bonds generated for 'chain 'B' and resid 321 through 323' Processing helix chain 'B' and resid 324 through 337 removed outlier: 3.651A pdb=" N MET B 328 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE B 331 " --> pdb=" O SER B 327 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA B 332 " --> pdb=" O MET B 328 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS B 335 " --> pdb=" O PHE B 331 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 removed outlier: 3.726A pdb=" N ASP B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 417 Processing helix chain 'B' and resid 433 through 437 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 472 through 483 Processing helix chain 'B' and resid 485 through 492 removed outlier: 3.568A pdb=" N ILE B 490 " --> pdb=" O HIS B 486 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 497 removed outlier: 3.626A pdb=" N ASP B 497 " --> pdb=" O ASP B 494 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 494 through 497' Processing helix chain 'B' and resid 508 through 524 removed outlier: 3.506A pdb=" N ASN B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 554 removed outlier: 3.520A pdb=" N LEU B 544 " --> pdb=" O GLU B 540 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 571 removed outlier: 3.774A pdb=" N ILE B 568 " --> pdb=" O ARG B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 593 removed outlier: 3.852A pdb=" N PHE B 592 " --> pdb=" O HIS B 588 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 603 removed outlier: 3.516A pdb=" N LYS B 602 " --> pdb=" O GLY B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 613 removed outlier: 3.636A pdb=" N ALA B 609 " --> pdb=" O LYS B 605 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA B 610 " --> pdb=" O MET B 606 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N HIS B 611 " --> pdb=" O GLN B 607 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU B 612 " --> pdb=" O GLU B 608 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 613 " --> pdb=" O ALA B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 693 removed outlier: 3.844A pdb=" N ASN B 684 " --> pdb=" O LYS B 680 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER B 685 " --> pdb=" O ASP B 681 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE B 686 " --> pdb=" O GLN B 682 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET B 692 " --> pdb=" O ARG B 688 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN B 693 " --> pdb=" O LEU B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 728 removed outlier: 4.134A pdb=" N LEU B 725 " --> pdb=" O LEU B 721 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 750 removed outlier: 4.003A pdb=" N LYS B 738 " --> pdb=" O GLU B 734 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN B 739 " --> pdb=" O TYR B 735 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 747 " --> pdb=" O TYR B 743 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE B 748 " --> pdb=" O CYS B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 762 removed outlier: 3.586A pdb=" N PHE B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 760 " --> pdb=" O VAL B 756 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN B 761 " --> pdb=" O PHE B 757 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS B 762 " --> pdb=" O ASN B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 780 removed outlier: 3.903A pdb=" N VAL B 768 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 769 " --> pdb=" O TRP B 765 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 770 " --> pdb=" O ASP B 766 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 772 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS B 774 " --> pdb=" O GLU B 770 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU B 778 " --> pdb=" O LYS B 774 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET B 780 " --> pdb=" O VAL B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 785 Processing helix chain 'B' and resid 786 through 787 No H-bonds generated for 'chain 'B' and resid 786 through 787' Processing helix chain 'B' and resid 788 through 794 removed outlier: 3.821A pdb=" N GLN B 794 " --> pdb=" O TRP B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 809 removed outlier: 3.949A pdb=" N ILE B 802 " --> pdb=" O GLU B 798 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA B 803 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA B 804 " --> pdb=" O ALA B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 829 removed outlier: 3.801A pdb=" N SER B 822 " --> pdb=" O GLY B 818 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL B 823 " --> pdb=" O ASP B 819 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN B 826 " --> pdb=" O SER B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 842 removed outlier: 3.862A pdb=" N THR B 836 " --> pdb=" O LEU B 832 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 837 " --> pdb=" O VAL B 833 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 852 removed outlier: 4.150A pdb=" N VAL B 848 " --> pdb=" O ARG B 844 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 850 " --> pdb=" O ALA B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 862 removed outlier: 3.533A pdb=" N ALA B 859 " --> pdb=" O VAL B 855 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 862 " --> pdb=" O ALA B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 878 removed outlier: 4.028A pdb=" N ALA B 877 " --> pdb=" O ASP B 873 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS B 878 " --> pdb=" O LEU B 874 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 873 through 878' Processing helix chain 'B' and resid 880 through 889 removed outlier: 4.218A pdb=" N LEU B 884 " --> pdb=" O LYS B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 898 removed outlier: 3.814A pdb=" N PHE B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 910 Processing helix chain 'B' and resid 912 through 917 Processing helix chain 'B' and resid 918 through 939 removed outlier: 3.542A pdb=" N GLY B 923 " --> pdb=" O CYS B 919 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR B 930 " --> pdb=" O ALA B 926 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU B 937 " --> pdb=" O ALA B 933 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 938 " --> pdb=" O GLN B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 954 removed outlier: 3.810A pdb=" N GLY B 944 " --> pdb=" O SER B 940 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU B 945 " --> pdb=" O TYR B 941 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TRP B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS B 954 " --> pdb=" O TRP B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 972 removed outlier: 4.028A pdb=" N ARG B 964 " --> pdb=" O SER B 960 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 965 " --> pdb=" O LYS B 961 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE B 966 " --> pdb=" O THR B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 980 removed outlier: 4.284A pdb=" N THR B 979 " --> pdb=" O ALA B 976 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 980 " --> pdb=" O ALA B 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 976 through 980' Processing helix chain 'B' and resid 988 through 1001 removed outlier: 4.607A pdb=" N SER B 995 " --> pdb=" O GLN B 991 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1073 Processing helix chain 'B' and resid 1089 through 1093 removed outlier: 3.644A pdb=" N LYS B1092 " --> pdb=" O ASP B1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1099 removed outlier: 3.561A pdb=" N ILE B1098 " --> pdb=" O ASN B1094 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG B1099 " --> pdb=" O LEU B1095 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1094 through 1099' Processing helix chain 'B' and resid 1115 through 1121 Processing helix chain 'B' and resid 1128 through 1139 Processing helix chain 'B' and resid 1141 through 1148 Processing helix chain 'B' and resid 1164 through 1177 removed outlier: 3.841A pdb=" N ARG B1170 " --> pdb=" O GLY B1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 1194 through 1209 removed outlier: 3.762A pdb=" N SER B1200 " --> pdb=" O GLU B1196 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU B1203 " --> pdb=" O ARG B1199 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1225 Processing helix chain 'B' and resid 1243 through 1251 Processing helix chain 'B' and resid 1254 through 1259 Processing helix chain 'B' and resid 1260 through 1263 removed outlier: 4.454A pdb=" N GLN B1263 " --> pdb=" O ILE B1260 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1260 through 1263' Processing sheet with id=AA1, first strand: chain 'B' and resid 386 through 393 removed outlier: 7.014A pdb=" N ASN B 387 " --> pdb=" O ASP B 374 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP B 374 " --> pdb=" O ASN B 387 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N PHE B 389 " --> pdb=" O ASN B 372 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU B 370 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU B 428 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASN B 372 " --> pdb=" O GLN B 426 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLN B 426 " --> pdb=" O ASN B 372 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 446 through 449 removed outlier: 3.601A pdb=" N ASP B 531 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B 528 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE B 561 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU B 530 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL B 402 " --> pdb=" O ALA B 575 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 577 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N GLN B 578 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL B 582 " --> pdb=" O GLN B 578 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 458 through 459 Processing sheet with id=AA4, first strand: chain 'B' and resid 1042 through 1048 removed outlier: 6.733A pdb=" N ARG B1043 " --> pdb=" O ASP B1030 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP B1030 " --> pdb=" O ARG B1043 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU B1045 " --> pdb=" O HIS B1028 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B1047 " --> pdb=" O LEU B1026 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE B1029 " --> pdb=" O SER B1080 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER B1080 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1057 through 1058 removed outlier: 4.291A pdb=" N GLU B1240 " --> pdb=" O VAL B1232 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASP B1234 " --> pdb=" O VAL B1238 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N VAL B1238 " --> pdb=" O ASP B1234 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1102 through 1105 removed outlier: 6.714A pdb=" N ALA B1103 " --> pdb=" O LEU B1185 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B1186 " --> pdb=" O ILE B1215 " (cutoff:3.500A) 347 hydrogen bonds defined for protein. 993 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1496 1.32 - 1.44: 2402 1.44 - 1.57: 5302 1.57 - 1.69: 1 1.69 - 1.82: 72 Bond restraints: 9273 Sorted by residual: bond pdb=" CB PRO B1015 " pdb=" CG PRO B1015 " ideal model delta sigma weight residual 1.492 1.594 -0.102 5.00e-02 4.00e+02 4.19e+00 bond pdb=" C ARG B 380 " pdb=" N PRO B 381 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.50e+00 bond pdb=" C PRO B 914 " pdb=" N PRO B 915 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.23e-02 6.61e+03 2.17e+00 bond pdb=" CB PRO B 381 " pdb=" CG PRO B 381 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 1.99e+00 bond pdb=" CB ASN B 811 " pdb=" CG ASN B 811 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.46e+00 ... (remaining 9268 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 12433 3.15 - 6.30: 111 6.30 - 9.46: 8 9.46 - 12.61: 4 12.61 - 15.76: 1 Bond angle restraints: 12557 Sorted by residual: angle pdb=" C GLN B 451 " pdb=" N GLU B 452 " pdb=" CA GLU B 452 " ideal model delta sigma weight residual 122.31 106.55 15.76 2.34e+00 1.83e-01 4.54e+01 angle pdb=" CA PRO B 381 " pdb=" N PRO B 381 " pdb=" CD PRO B 381 " ideal model delta sigma weight residual 112.00 105.36 6.64 1.40e+00 5.10e-01 2.25e+01 angle pdb=" N SER B 751 " pdb=" CA SER B 751 " pdb=" C SER B 751 " ideal model delta sigma weight residual 113.88 108.45 5.43 1.23e+00 6.61e-01 1.95e+01 angle pdb=" N VAL B 823 " pdb=" CA VAL B 823 " pdb=" C VAL B 823 " ideal model delta sigma weight residual 112.96 108.76 4.20 1.00e+00 1.00e+00 1.76e+01 angle pdb=" CA PRO B1015 " pdb=" N PRO B1015 " pdb=" CD PRO B1015 " ideal model delta sigma weight residual 112.00 106.25 5.75 1.40e+00 5.10e-01 1.69e+01 ... (remaining 12552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5057 17.97 - 35.93: 449 35.93 - 53.90: 83 53.90 - 71.86: 10 71.86 - 89.83: 7 Dihedral angle restraints: 5606 sinusoidal: 2212 harmonic: 3394 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 180.00 150.28 29.72 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA LYS B 988 " pdb=" C LYS B 988 " pdb=" N GLY B 989 " pdb=" CA GLY B 989 " ideal model delta harmonic sigma weight residual 180.00 157.74 22.26 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA ASP B 985 " pdb=" C ASP B 985 " pdb=" N PHE B 986 " pdb=" CA PHE B 986 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 5603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1229 0.057 - 0.115: 211 0.115 - 0.172: 13 0.172 - 0.229: 2 0.229 - 0.287: 2 Chirality restraints: 1457 Sorted by residual: chirality pdb=" C10 BLD B1301 " pdb=" C01 BLD B1301 " pdb=" C05 BLD B1301 " pdb=" C09 BLD B1301 " both_signs ideal model delta sigma weight residual False -3.02 -2.73 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CG LEU B1177 " pdb=" CB LEU B1177 " pdb=" CD1 LEU B1177 " pdb=" CD2 LEU B1177 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB ILE B1085 " pdb=" CA ILE B1085 " pdb=" CG1 ILE B1085 " pdb=" CG2 ILE B1085 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.59e-01 ... (remaining 1454 not shown) Planarity restraints: 1588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 380 " 0.090 5.00e-02 4.00e+02 1.35e-01 2.92e+01 pdb=" N PRO B 381 " -0.234 5.00e-02 4.00e+02 pdb=" CA PRO B 381 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 381 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B1014 " -0.055 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO B1015 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B1015 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B1015 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 694 " 0.050 5.00e-02 4.00e+02 7.52e-02 9.04e+00 pdb=" N PRO B 695 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 695 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 695 " 0.041 5.00e-02 4.00e+02 ... (remaining 1585 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 155 2.68 - 3.23: 8684 3.23 - 3.79: 12980 3.79 - 4.34: 18237 4.34 - 4.90: 29225 Nonbonded interactions: 69281 Sorted by model distance: nonbonded pdb=" OG1 THR B1115 " pdb=" OE1 GLU B1118 " model vdw 2.123 3.040 nonbonded pdb=" OG1 THR B 458 " pdb=" OE1 GLU B 462 " model vdw 2.171 3.040 nonbonded pdb=" OG1 THR B1014 " pdb=" O LYS B1092 " model vdw 2.213 3.040 nonbonded pdb=" O VAL B 482 " pdb=" NH2 ARG B 551 " model vdw 2.214 3.120 nonbonded pdb=" OD1 ASP B 766 " pdb=" NH2 ARG B 814 " model vdw 2.216 3.120 ... (remaining 69276 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: 1.440 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.740 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 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 : 0.003 0.102 9273 Z= 0.153 Angle : 0.774 15.759 12557 Z= 0.439 Chirality : 0.043 0.287 1457 Planarity : 0.006 0.135 1588 Dihedral : 14.100 89.830 3422 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.31 % Allowed : 14.61 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.25 (0.22), residues: 1174 helix: -2.40 (0.18), residues: 658 sheet: 0.03 (0.85), residues: 45 loop : -1.76 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1225 TYR 0.017 0.001 TYR B1155 PHE 0.028 0.001 PHE B 137 TRP 0.017 0.001 TRP B 687 HIS 0.006 0.001 HIS B1228 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9273) covalent geometry : angle 0.77356 (12557) hydrogen bonds : bond 0.26012 ( 347) hydrogen bonds : angle 8.88869 ( 993) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 118 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 PHE cc_start: 0.8380 (t80) cc_final: 0.8128 (t80) REVERT: B 928 SER cc_start: 0.8865 (m) cc_final: 0.8625 (t) outliers start: 3 outliers final: 2 residues processed: 119 average time/residue: 0.1018 time to fit residues: 16.6449 Evaluate side-chains 113 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 1038 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.0070 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 578 GLN B 911 ASN B1246 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.192945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.122616 restraints weight = 11483.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126259 restraints weight = 6932.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.126973 restraints weight = 4555.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126843 restraints weight = 3902.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.127198 restraints weight = 4218.797| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9273 Z= 0.119 Angle : 0.575 8.444 12557 Z= 0.302 Chirality : 0.041 0.183 1457 Planarity : 0.005 0.078 1588 Dihedral : 6.006 43.370 1356 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.46 % Allowed : 13.26 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.85 (0.23), residues: 1174 helix: -2.02 (0.18), residues: 687 sheet: -0.16 (0.78), residues: 48 loop : -1.57 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 801 TYR 0.017 0.001 TYR B 728 PHE 0.012 0.001 PHE B 149 TRP 0.010 0.001 TRP B 687 HIS 0.004 0.001 HIS B1228 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9273) covalent geometry : angle 0.57548 (12557) hydrogen bonds : bond 0.03810 ( 347) hydrogen bonds : angle 5.26996 ( 993) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 546 GLN cc_start: 0.8639 (tp-100) cc_final: 0.8280 (tp-100) REVERT: B 1188 GLU cc_start: 0.7493 (pt0) cc_final: 0.7060 (pp20) outliers start: 14 outliers final: 7 residues processed: 140 average time/residue: 0.1163 time to fit residues: 21.6813 Evaluate side-chains 119 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1217 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 797 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.186107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.128269 restraints weight = 11645.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.122009 restraints weight = 14714.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.118024 restraints weight = 9406.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117494 restraints weight = 9353.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.118111 restraints weight = 7115.832| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9273 Z= 0.269 Angle : 0.689 14.614 12557 Z= 0.355 Chirality : 0.045 0.176 1457 Planarity : 0.005 0.073 1588 Dihedral : 6.270 42.164 1351 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.55 % Allowed : 12.63 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.90 (0.23), residues: 1174 helix: -2.02 (0.18), residues: 706 sheet: -0.38 (0.71), residues: 53 loop : -1.62 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 801 TYR 0.019 0.002 TYR B1122 PHE 0.025 0.002 PHE B 72 TRP 0.012 0.002 TRP B 843 HIS 0.005 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00639 ( 9273) covalent geometry : angle 0.68922 (12557) hydrogen bonds : bond 0.04835 ( 347) hydrogen bonds : angle 5.16695 ( 993) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.319 Fit side-chains REVERT: B 83 MET cc_start: 0.8046 (tpp) cc_final: 0.7493 (tpp) REVERT: B 225 GLN cc_start: 0.7850 (tt0) cc_final: 0.7588 (tt0) REVERT: B 546 GLN cc_start: 0.8637 (tp-100) cc_final: 0.8232 (tp-100) REVERT: B 788 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6414 (mp0) REVERT: B 849 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7596 (mm) REVERT: B 1048 ARG cc_start: 0.7507 (ttm110) cc_final: 0.7249 (ttm110) REVERT: B 1100 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8558 (mmtt) REVERT: B 1134 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7678 (tm-30) REVERT: B 1177 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8111 (mm) REVERT: B 1188 GLU cc_start: 0.7761 (pt0) cc_final: 0.7044 (pp20) REVERT: B 1259 MET cc_start: 0.8556 (mmm) cc_final: 0.8292 (mmm) outliers start: 34 outliers final: 19 residues processed: 142 average time/residue: 0.0961 time to fit residues: 19.1244 Evaluate side-chains 132 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 687 TRP Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain B residue 892 VAL Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1177 LEU Chi-restraints excluded: chain B residue 1178 VAL Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1216 VAL Chi-restraints excluded: chain B residue 1217 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 43 optimal weight: 0.0470 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 106 optimal weight: 0.0970 chunk 114 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 69 optimal weight: 0.0570 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.193459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123670 restraints weight = 11710.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.126068 restraints weight = 6812.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.126700 restraints weight = 4827.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128489 restraints weight = 4083.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.128395 restraints weight = 3971.636| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9273 Z= 0.097 Angle : 0.557 10.834 12557 Z= 0.284 Chirality : 0.040 0.182 1457 Planarity : 0.004 0.060 1588 Dihedral : 5.409 41.319 1351 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.51 % Allowed : 14.20 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.24), residues: 1174 helix: -1.56 (0.19), residues: 688 sheet: 0.03 (0.72), residues: 53 loop : -1.60 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1225 TYR 0.007 0.001 TYR B1122 PHE 0.011 0.001 PHE B 149 TRP 0.010 0.001 TRP B 946 HIS 0.005 0.001 HIS B1228 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 9273) covalent geometry : angle 0.55726 (12557) hydrogen bonds : bond 0.02983 ( 347) hydrogen bonds : angle 4.42808 ( 993) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.352 Fit side-chains REVERT: B 546 GLN cc_start: 0.8610 (tp-100) cc_final: 0.8201 (tp-100) REVERT: B 770 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: B 788 GLU cc_start: 0.6200 (OUTLIER) cc_final: 0.5894 (mp0) REVERT: B 1084 MET cc_start: 0.7895 (mtm) cc_final: 0.7635 (ptp) REVERT: B 1108 GLU cc_start: 0.7341 (tp30) cc_final: 0.7122 (tp30) REVERT: B 1134 GLN cc_start: 0.7773 (tm-30) cc_final: 0.7401 (pp30) REVERT: B 1177 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7947 (mm) REVERT: B 1188 GLU cc_start: 0.7424 (pt0) cc_final: 0.6999 (pp20) REVERT: B 1207 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8701 (mp10) outliers start: 24 outliers final: 11 residues processed: 133 average time/residue: 0.0977 time to fit residues: 18.1289 Evaluate side-chains 126 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 687 TRP Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 TYR Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1177 LEU Chi-restraints excluded: chain B residue 1207 GLN Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1217 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 578 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.185115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128078 restraints weight = 11706.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.120229 restraints weight = 14695.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114773 restraints weight = 9519.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114278 restraints weight = 10708.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115777 restraints weight = 8168.308| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9273 Z= 0.258 Angle : 0.677 14.730 12557 Z= 0.345 Chirality : 0.045 0.151 1457 Planarity : 0.005 0.068 1588 Dihedral : 6.007 41.967 1351 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.13 % Allowed : 15.76 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.54 (0.24), residues: 1174 helix: -1.76 (0.19), residues: 699 sheet: 0.17 (0.72), residues: 53 loop : -1.49 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1258 TYR 0.018 0.002 TYR B1122 PHE 0.027 0.002 PHE B 72 TRP 0.015 0.002 TRP B 291 HIS 0.004 0.001 HIS B1228 Details of bonding type rmsd covalent geometry : bond 0.00613 ( 9273) covalent geometry : angle 0.67685 (12557) hydrogen bonds : bond 0.04476 ( 347) hydrogen bonds : angle 4.82470 ( 993) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: B 225 GLN cc_start: 0.7871 (tt0) cc_final: 0.7635 (tt0) REVERT: B 546 GLN cc_start: 0.8621 (tp-100) cc_final: 0.8199 (tp-100) REVERT: B 770 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7389 (mt-10) REVERT: B 788 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6353 (mp0) REVERT: B 849 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7675 (mm) REVERT: B 1084 MET cc_start: 0.7632 (mtm) cc_final: 0.7422 (ptp) REVERT: B 1108 GLU cc_start: 0.7618 (tp30) cc_final: 0.7385 (tp30) REVERT: B 1118 GLU cc_start: 0.8179 (mp0) cc_final: 0.7971 (mp0) REVERT: B 1134 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7502 (pp30) REVERT: B 1177 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8070 (mm) REVERT: B 1188 GLU cc_start: 0.7533 (pt0) cc_final: 0.7034 (pp20) REVERT: B 1207 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8790 (mp10) REVERT: B 1220 ARG cc_start: 0.8597 (tpm170) cc_final: 0.8367 (tpm170) outliers start: 30 outliers final: 21 residues processed: 135 average time/residue: 0.0982 time to fit residues: 18.5055 Evaluate side-chains 135 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 311 MET Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1177 LEU Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain B residue 1207 GLN Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1217 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 75 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.190681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119049 restraints weight = 11630.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.122555 restraints weight = 6956.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123544 restraints weight = 4690.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.123737 restraints weight = 3900.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124093 restraints weight = 4087.633| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9273 Z= 0.112 Angle : 0.569 12.939 12557 Z= 0.288 Chirality : 0.041 0.152 1457 Planarity : 0.004 0.063 1588 Dihedral : 5.487 40.987 1351 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.92 % Allowed : 15.87 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.24), residues: 1174 helix: -1.46 (0.19), residues: 693 sheet: 0.48 (0.75), residues: 53 loop : -1.50 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1225 TYR 0.010 0.001 TYR B1122 PHE 0.015 0.001 PHE B1144 TRP 0.015 0.001 TRP B 291 HIS 0.005 0.001 HIS B1228 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9273) covalent geometry : angle 0.56877 (12557) hydrogen bonds : bond 0.03189 ( 347) hydrogen bonds : angle 4.34437 ( 993) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: B 225 GLN cc_start: 0.7826 (tt0) cc_final: 0.7570 (tt0) REVERT: B 236 GLN cc_start: 0.8590 (mt0) cc_final: 0.8341 (mt0) REVERT: B 546 GLN cc_start: 0.8602 (tp-100) cc_final: 0.8153 (tp-100) REVERT: B 578 GLN cc_start: 0.8211 (tp-100) cc_final: 0.7691 (tp40) REVERT: B 770 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7129 (mt-10) REVERT: B 788 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.6104 (mp0) REVERT: B 849 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7581 (mm) REVERT: B 1108 GLU cc_start: 0.7599 (tp30) cc_final: 0.7336 (tp30) REVERT: B 1134 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7437 (pp30) REVERT: B 1177 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7963 (mm) REVERT: B 1188 GLU cc_start: 0.7435 (pt0) cc_final: 0.7066 (pp20) REVERT: B 1207 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8792 (mp10) REVERT: B 1220 ARG cc_start: 0.8706 (tpm170) cc_final: 0.8411 (tpm170) outliers start: 28 outliers final: 17 residues processed: 133 average time/residue: 0.1009 time to fit residues: 18.9043 Evaluate side-chains 132 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 MET Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 687 TRP Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 TYR Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1177 LEU Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain B residue 1207 GLN Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1217 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 69 optimal weight: 0.2980 chunk 80 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 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 486 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.191030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.140550 restraints weight = 11629.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.136576 restraints weight = 23767.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.138927 restraints weight = 19722.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138969 restraints weight = 10770.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.140149 restraints weight = 9461.180| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9273 Z= 0.111 Angle : 0.564 12.824 12557 Z= 0.283 Chirality : 0.040 0.152 1457 Planarity : 0.004 0.059 1588 Dihedral : 5.293 40.792 1351 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.92 % Allowed : 16.08 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.24), residues: 1174 helix: -1.24 (0.20), residues: 690 sheet: 0.69 (0.76), residues: 53 loop : -1.44 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 994 TYR 0.011 0.001 TYR B1155 PHE 0.014 0.001 PHE B 72 TRP 0.018 0.001 TRP B 291 HIS 0.006 0.001 HIS B1228 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9273) covalent geometry : angle 0.56357 (12557) hydrogen bonds : bond 0.03067 ( 347) hydrogen bonds : angle 4.21695 ( 993) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: B 225 GLN cc_start: 0.7747 (tt0) cc_final: 0.7459 (tt0) REVERT: B 546 GLN cc_start: 0.8055 (tp-100) cc_final: 0.7598 (tp-100) REVERT: B 578 GLN cc_start: 0.7650 (tp-100) cc_final: 0.7173 (tp-100) REVERT: B 716 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.7168 (m-80) REVERT: B 770 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7232 (mt-10) REVERT: B 788 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6257 (mp0) REVERT: B 801 ARG cc_start: 0.7575 (mtm110) cc_final: 0.7361 (mtm110) REVERT: B 849 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7220 (mm) REVERT: B 1048 ARG cc_start: 0.7308 (ttm110) cc_final: 0.7076 (ttm110) REVERT: B 1134 GLN cc_start: 0.7394 (tm-30) cc_final: 0.7102 (pp30) REVERT: B 1177 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7948 (mm) outliers start: 28 outliers final: 19 residues processed: 127 average time/residue: 0.1067 time to fit residues: 18.7534 Evaluate side-chains 127 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 MET Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 687 TRP Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 716 PHE Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 TYR Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1177 LEU Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1217 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 95 optimal weight: 20.0000 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 116 optimal weight: 30.0000 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.191142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.137924 restraints weight = 11563.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.133308 restraints weight = 21170.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.135736 restraints weight = 18059.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.135637 restraints weight = 10252.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.138320 restraints weight = 8820.746| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9273 Z= 0.119 Angle : 0.580 11.704 12557 Z= 0.293 Chirality : 0.041 0.140 1457 Planarity : 0.004 0.061 1588 Dihedral : 5.225 40.440 1351 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.92 % Allowed : 16.49 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.24), residues: 1174 helix: -1.14 (0.20), residues: 691 sheet: 0.77 (0.77), residues: 53 loop : -1.46 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 994 TYR 0.010 0.001 TYR B1122 PHE 0.017 0.001 PHE B 149 TRP 0.019 0.001 TRP B 291 HIS 0.005 0.001 HIS B1228 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9273) covalent geometry : angle 0.58042 (12557) hydrogen bonds : bond 0.03096 ( 347) hydrogen bonds : angle 4.20546 ( 993) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: B 546 GLN cc_start: 0.8198 (tp-100) cc_final: 0.7719 (tp-100) REVERT: B 578 GLN cc_start: 0.7768 (tp-100) cc_final: 0.7277 (tp-100) REVERT: B 716 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.7146 (m-80) REVERT: B 770 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: B 788 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.6218 (mp0) REVERT: B 801 ARG cc_start: 0.7623 (mtm110) cc_final: 0.7369 (mtm110) REVERT: B 849 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7402 (mm) REVERT: B 1048 ARG cc_start: 0.7242 (ttm110) cc_final: 0.7011 (ttm110) REVERT: B 1100 LYS cc_start: 0.8449 (mmmt) cc_final: 0.8118 (mmmt) REVERT: B 1134 GLN cc_start: 0.7472 (tm-30) cc_final: 0.7176 (pp30) REVERT: B 1177 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7957 (mm) outliers start: 28 outliers final: 18 residues processed: 129 average time/residue: 0.1102 time to fit residues: 19.3489 Evaluate side-chains 124 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 MET Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 687 TRP Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 716 PHE Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 TYR Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1177 LEU Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1217 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 93 optimal weight: 0.4980 chunk 7 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.192362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.141963 restraints weight = 11560.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.140642 restraints weight = 23206.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.142154 restraints weight = 18203.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.141940 restraints weight = 10692.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.143644 restraints weight = 8821.070| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9273 Z= 0.103 Angle : 0.590 16.162 12557 Z= 0.292 Chirality : 0.040 0.145 1457 Planarity : 0.004 0.057 1588 Dihedral : 5.086 40.737 1351 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.71 % Allowed : 16.81 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.25), residues: 1174 helix: -1.01 (0.20), residues: 692 sheet: 0.67 (0.71), residues: 63 loop : -1.38 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 994 TYR 0.012 0.001 TYR B1155 PHE 0.018 0.001 PHE B 686 TRP 0.020 0.001 TRP B 291 HIS 0.006 0.001 HIS B1228 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 9273) covalent geometry : angle 0.59032 (12557) hydrogen bonds : bond 0.02845 ( 347) hydrogen bonds : angle 4.08904 ( 993) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 367 LEU cc_start: 0.7751 (tp) cc_final: 0.7539 (mt) REVERT: B 578 GLN cc_start: 0.7627 (tp-100) cc_final: 0.7309 (tp40) REVERT: B 716 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.7184 (m-80) REVERT: B 750 LEU cc_start: 0.7245 (pp) cc_final: 0.6693 (mt) REVERT: B 770 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7103 (mt-10) REVERT: B 788 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6248 (mp0) REVERT: B 801 ARG cc_start: 0.7598 (mtm110) cc_final: 0.7382 (mtm110) REVERT: B 849 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.6961 (mm) REVERT: B 889 ILE cc_start: 0.8906 (tt) cc_final: 0.8609 (tt) REVERT: B 1048 ARG cc_start: 0.7193 (ttm110) cc_final: 0.6963 (ttm110) REVERT: B 1100 LYS cc_start: 0.8510 (mmmt) cc_final: 0.8135 (mmmt) REVERT: B 1134 GLN cc_start: 0.7425 (tm-30) cc_final: 0.7148 (pp30) REVERT: B 1177 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7915 (mm) outliers start: 26 outliers final: 17 residues processed: 137 average time/residue: 0.1039 time to fit residues: 19.4930 Evaluate side-chains 133 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 MET Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 716 PHE Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 TYR Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1177 LEU Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1217 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 91 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 50 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.185672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.128578 restraints weight = 11684.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.120130 restraints weight = 15643.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114302 restraints weight = 10048.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114836 restraints weight = 8647.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.115527 restraints weight = 7099.771| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9273 Z= 0.258 Angle : 0.696 15.474 12557 Z= 0.351 Chirality : 0.045 0.169 1457 Planarity : 0.005 0.068 1588 Dihedral : 5.774 41.505 1351 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.51 % Allowed : 17.43 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.24), residues: 1174 helix: -1.41 (0.19), residues: 699 sheet: 0.59 (0.80), residues: 46 loop : -1.31 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1225 TYR 0.017 0.002 TYR B1122 PHE 0.031 0.003 PHE B 72 TRP 0.026 0.002 TRP B 291 HIS 0.006 0.001 HIS B1228 Details of bonding type rmsd covalent geometry : bond 0.00614 ( 9273) covalent geometry : angle 0.69581 (12557) hydrogen bonds : bond 0.04295 ( 347) hydrogen bonds : angle 4.57149 ( 993) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 225 GLN cc_start: 0.7950 (tt0) cc_final: 0.7627 (tt0) REVERT: B 546 GLN cc_start: 0.8668 (tp-100) cc_final: 0.8190 (tp-100) REVERT: B 716 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.7326 (m-80) REVERT: B 770 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7272 (mt-10) REVERT: B 788 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6419 (mp0) REVERT: B 849 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7649 (mm) REVERT: B 889 ILE cc_start: 0.8920 (tt) cc_final: 0.8642 (tt) REVERT: B 1048 ARG cc_start: 0.7540 (ttm110) cc_final: 0.7233 (ttm110) REVERT: B 1100 LYS cc_start: 0.8721 (mmmt) cc_final: 0.8304 (mmmt) REVERT: B 1134 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7568 (pp30) REVERT: B 1177 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8008 (mm) REVERT: B 1225 ARG cc_start: 0.8135 (mmm160) cc_final: 0.7903 (mmm160) outliers start: 24 outliers final: 16 residues processed: 128 average time/residue: 0.1009 time to fit residues: 17.9407 Evaluate side-chains 130 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 MET Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 716 PHE Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 TYR Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1177 LEU Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1217 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 93 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 88 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.190940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.140421 restraints weight = 11389.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.138867 restraints weight = 23528.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.140244 restraints weight = 19273.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.140400 restraints weight = 10665.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.141409 restraints weight = 9210.556| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9273 Z= 0.107 Angle : 0.594 15.158 12557 Z= 0.296 Chirality : 0.041 0.157 1457 Planarity : 0.004 0.057 1588 Dihedral : 5.239 41.242 1351 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.51 % Allowed : 18.16 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.25), residues: 1174 helix: -1.04 (0.20), residues: 691 sheet: 0.69 (0.70), residues: 63 loop : -1.35 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1225 TYR 0.013 0.001 TYR B1155 PHE 0.019 0.001 PHE B 686 TRP 0.020 0.001 TRP B 291 HIS 0.006 0.001 HIS B1228 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9273) covalent geometry : angle 0.59427 (12557) hydrogen bonds : bond 0.02967 ( 347) hydrogen bonds : angle 4.16356 ( 993) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1598.36 seconds wall clock time: 28 minutes 17.25 seconds (1697.25 seconds total)